data_8JLE # _entry.id 8JLE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 8JLE pdb_00008jle 10.2210/pdb8jle/pdb WWPDB D_1300038170 ? ? EMDB EMD-36394 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2024-05-01 2 'Structure model' 1 1 2024-05-08 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 2 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category citation # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.page_last' 2 2 'Structure model' '_citation.pdbx_database_id_PubMed' 3 2 'Structure model' '_citation.title' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8JLE _pdbx_database_status.recvd_initial_deposition_date 2023-06-02 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the SV2A-levetiracetam-BoNT/A2 Hc complex' _pdbx_database_related.db_id EMD-36394 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 2 _pdbx_contact_author.email atsushi.yamagata@riken.jp _pdbx_contact_author.name_first Atsushi _pdbx_contact_author.name_last Yamagata _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-9285-1256 # _audit_author.name 'Yamagata, A.' _audit_author.pdbx_ordinal 1 _audit_author.identifier_ORCID 0000-0001-9285-1256 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 15 _citation.language ? _citation.page_first 3027 _citation.page_last 3027 _citation.title 'Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-024-47322-4 _citation.pdbx_database_id_PubMed 38637505 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yamagata, A.' 1 ? primary 'Ito, K.' 2 ? primary 'Suzuki, T.' 3 ? primary 'Dohmae, N.' 4 ? primary 'Terada, T.' 5 ? primary 'Shirouzu, M.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Synaptic vesicle glycoprotein 2A' 12797.238 1 ? ? ? ? 2 polymer man 'Botulinum neurotoxin' 49456.191 1 ? ? ? ? 3 branched man '2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose' 570.542 1 ? ? ? ? 4 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 2 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;YASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSSNTFFRNCTFINTVFYNT DLFEYKFVNSRLINSTFLHNKEGCPLDV ; ;YASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSSNTFFRNCTFINTVFYNT DLFEYKFVNSRLINSTFLHNKEGCPLDV ; A ? 2 'polypeptide(L)' no no ;KNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKNAIVYNSMYENFSTSFWIKIP KYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDNKQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIY INGRLIDQKPISNLGNIHASNKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKP YYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNEDNIVRNNDRVYINVVVKNKE YRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQGIRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQ VGKASRTFGCSWEFIPVDDGWGESSL ; ;KNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKNAIVYNSMYENFSTSFWIKIP KYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDNKQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIY INGRLIDQKPISNLGNIHASNKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKP YYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNEDNIVRNNDRVYINVVVKNKE YRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQGIRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQ VGKASRTFGCSWEFIPVDDGWGESSL ; B ? # _pdbx_entity_nonpoly.entity_id 4 _pdbx_entity_nonpoly.name 2-acetamido-2-deoxy-beta-D-glucopyranose _pdbx_entity_nonpoly.comp_id NAG # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 TYR n 1 2 ALA n 1 3 SER n 1 4 ARG n 1 5 THR n 1 6 LYS n 1 7 VAL n 1 8 PHE n 1 9 PRO n 1 10 GLY n 1 11 GLU n 1 12 ARG n 1 13 VAL n 1 14 GLU n 1 15 HIS n 1 16 VAL n 1 17 THR n 1 18 PHE n 1 19 ASN n 1 20 PHE n 1 21 THR n 1 22 LEU n 1 23 GLU n 1 24 ASN n 1 25 GLN n 1 26 ILE n 1 27 HIS n 1 28 ARG n 1 29 GLY n 1 30 GLY n 1 31 GLN n 1 32 TYR n 1 33 PHE n 1 34 ASN n 1 35 ASP n 1 36 LYS n 1 37 PHE n 1 38 ILE n 1 39 GLY n 1 40 LEU n 1 41 ARG n 1 42 LEU n 1 43 LYS n 1 44 SER n 1 45 VAL n 1 46 SER n 1 47 PHE n 1 48 GLU n 1 49 ASP n 1 50 SER n 1 51 LEU n 1 52 PHE n 1 53 GLU n 1 54 GLU n 1 55 CYS n 1 56 TYR n 1 57 PHE n 1 58 GLU n 1 59 ASP n 1 60 VAL n 1 61 THR n 1 62 SER n 1 63 SER n 1 64 ASN n 1 65 THR n 1 66 PHE n 1 67 PHE n 1 68 ARG n 1 69 ASN n 1 70 CYS n 1 71 THR n 1 72 PHE n 1 73 ILE n 1 74 ASN n 1 75 THR n 1 76 VAL n 1 77 PHE n 1 78 TYR n 1 79 ASN n 1 80 THR n 1 81 ASP n 1 82 LEU n 1 83 PHE n 1 84 GLU n 1 85 TYR n 1 86 LYS n 1 87 PHE n 1 88 VAL n 1 89 ASN n 1 90 SER n 1 91 ARG n 1 92 LEU n 1 93 ILE n 1 94 ASN n 1 95 SER n 1 96 THR n 1 97 PHE n 1 98 LEU n 1 99 HIS n 1 100 ASN n 1 101 LYS n 1 102 GLU n 1 103 GLY n 1 104 CYS n 1 105 PRO n 1 106 LEU n 1 107 ASP n 1 108 VAL n 2 1 LYS n 2 2 ASN n 2 3 ILE n 2 4 VAL n 2 5 ASN n 2 6 THR n 2 7 SER n 2 8 ILE n 2 9 LEU n 2 10 SER n 2 11 ILE n 2 12 VAL n 2 13 TYR n 2 14 LYS n 2 15 LYS n 2 16 ASP n 2 17 ASP n 2 18 LEU n 2 19 ILE n 2 20 ASP n 2 21 LEU n 2 22 SER n 2 23 ARG n 2 24 TYR n 2 25 GLY n 2 26 ALA n 2 27 LYS n 2 28 ILE n 2 29 ASN n 2 30 ILE n 2 31 GLY n 2 32 ASP n 2 33 ARG n 2 34 VAL n 2 35 TYR n 2 36 TYR n 2 37 ASP n 2 38 SER n 2 39 ILE n 2 40 ASP n 2 41 LYS n 2 42 ASN n 2 43 GLN n 2 44 ILE n 2 45 LYS n 2 46 LEU n 2 47 ILE n 2 48 ASN n 2 49 LEU n 2 50 GLU n 2 51 SER n 2 52 SER n 2 53 THR n 2 54 ILE n 2 55 GLU n 2 56 VAL n 2 57 ILE n 2 58 LEU n 2 59 LYS n 2 60 ASN n 2 61 ALA n 2 62 ILE n 2 63 VAL n 2 64 TYR n 2 65 ASN n 2 66 SER n 2 67 MET n 2 68 TYR n 2 69 GLU n 2 70 ASN n 2 71 PHE n 2 72 SER n 2 73 THR n 2 74 SER n 2 75 PHE n 2 76 TRP n 2 77 ILE n 2 78 LYS n 2 79 ILE n 2 80 PRO n 2 81 LYS n 2 82 TYR n 2 83 PHE n 2 84 SER n 2 85 LYS n 2 86 ILE n 2 87 ASN n 2 88 LEU n 2 89 ASN n 2 90 ASN n 2 91 GLU n 2 92 TYR n 2 93 THR n 2 94 ILE n 2 95 ILE n 2 96 ASN n 2 97 CYS n 2 98 ILE n 2 99 GLU n 2 100 ASN n 2 101 ASN n 2 102 SER n 2 103 GLY n 2 104 TRP n 2 105 LYS n 2 106 VAL n 2 107 SER n 2 108 LEU n 2 109 ASN n 2 110 TYR n 2 111 GLY n 2 112 GLU n 2 113 ILE n 2 114 ILE n 2 115 TRP n 2 116 THR n 2 117 LEU n 2 118 GLN n 2 119 ASP n 2 120 ASN n 2 121 LYS n 2 122 GLN n 2 123 ASN n 2 124 ILE n 2 125 GLN n 2 126 ARG n 2 127 VAL n 2 128 VAL n 2 129 PHE n 2 130 LYS n 2 131 TYR n 2 132 SER n 2 133 GLN n 2 134 MET n 2 135 VAL n 2 136 ASN n 2 137 ILE n 2 138 SER n 2 139 ASP n 2 140 TYR n 2 141 ILE n 2 142 ASN n 2 143 ARG n 2 144 TRP n 2 145 ILE n 2 146 PHE n 2 147 VAL n 2 148 THR n 2 149 ILE n 2 150 THR n 2 151 ASN n 2 152 ASN n 2 153 ARG n 2 154 LEU n 2 155 THR n 2 156 LYS n 2 157 SER n 2 158 LYS n 2 159 ILE n 2 160 TYR n 2 161 ILE n 2 162 ASN n 2 163 GLY n 2 164 ARG n 2 165 LEU n 2 166 ILE n 2 167 ASP n 2 168 GLN n 2 169 LYS n 2 170 PRO n 2 171 ILE n 2 172 SER n 2 173 ASN n 2 174 LEU n 2 175 GLY n 2 176 ASN n 2 177 ILE n 2 178 HIS n 2 179 ALA n 2 180 SER n 2 181 ASN n 2 182 LYS n 2 183 ILE n 2 184 MET n 2 185 PHE n 2 186 LYS n 2 187 LEU n 2 188 ASP n 2 189 GLY n 2 190 CYS n 2 191 ARG n 2 192 ASP n 2 193 PRO n 2 194 ARG n 2 195 ARG n 2 196 TYR n 2 197 ILE n 2 198 MET n 2 199 ILE n 2 200 LYS n 2 201 TYR n 2 202 PHE n 2 203 ASN n 2 204 LEU n 2 205 PHE n 2 206 ASP n 2 207 LYS n 2 208 GLU n 2 209 LEU n 2 210 ASN n 2 211 GLU n 2 212 LYS n 2 213 GLU n 2 214 ILE n 2 215 LYS n 2 216 ASP n 2 217 LEU n 2 218 TYR n 2 219 ASP n 2 220 SER n 2 221 GLN n 2 222 SER n 2 223 ASN n 2 224 SER n 2 225 GLY n 2 226 ILE n 2 227 LEU n 2 228 LYS n 2 229 ASP n 2 230 PHE n 2 231 TRP n 2 232 GLY n 2 233 ASN n 2 234 TYR n 2 235 LEU n 2 236 GLN n 2 237 TYR n 2 238 ASP n 2 239 LYS n 2 240 PRO n 2 241 TYR n 2 242 TYR n 2 243 MET n 2 244 LEU n 2 245 ASN n 2 246 LEU n 2 247 PHE n 2 248 ASP n 2 249 PRO n 2 250 ASN n 2 251 LYS n 2 252 TYR n 2 253 VAL n 2 254 ASP n 2 255 VAL n 2 256 ASN n 2 257 ASN n 2 258 ILE n 2 259 GLY n 2 260 ILE n 2 261 ARG n 2 262 GLY n 2 263 TYR n 2 264 MET n 2 265 TYR n 2 266 LEU n 2 267 LYS n 2 268 GLY n 2 269 PRO n 2 270 ARG n 2 271 GLY n 2 272 SER n 2 273 VAL n 2 274 VAL n 2 275 THR n 2 276 THR n 2 277 ASN n 2 278 ILE n 2 279 TYR n 2 280 LEU n 2 281 ASN n 2 282 SER n 2 283 THR n 2 284 LEU n 2 285 TYR n 2 286 GLU n 2 287 GLY n 2 288 THR n 2 289 LYS n 2 290 PHE n 2 291 ILE n 2 292 ILE n 2 293 LYS n 2 294 LYS n 2 295 TYR n 2 296 ALA n 2 297 SER n 2 298 GLY n 2 299 ASN n 2 300 GLU n 2 301 ASP n 2 302 ASN n 2 303 ILE n 2 304 VAL n 2 305 ARG n 2 306 ASN n 2 307 ASN n 2 308 ASP n 2 309 ARG n 2 310 VAL n 2 311 TYR n 2 312 ILE n 2 313 ASN n 2 314 VAL n 2 315 VAL n 2 316 VAL n 2 317 LYS n 2 318 ASN n 2 319 LYS n 2 320 GLU n 2 321 TYR n 2 322 ARG n 2 323 LEU n 2 324 ALA n 2 325 THR n 2 326 ASN n 2 327 ALA n 2 328 SER n 2 329 GLN n 2 330 ALA n 2 331 GLY n 2 332 VAL n 2 333 GLU n 2 334 LYS n 2 335 ILE n 2 336 LEU n 2 337 SER n 2 338 ALA n 2 339 LEU n 2 340 GLU n 2 341 ILE n 2 342 PRO n 2 343 ASP n 2 344 VAL n 2 345 GLY n 2 346 ASN n 2 347 LEU n 2 348 SER n 2 349 GLN n 2 350 VAL n 2 351 VAL n 2 352 VAL n 2 353 MET n 2 354 LYS n 2 355 SER n 2 356 LYS n 2 357 ASP n 2 358 ASP n 2 359 GLN n 2 360 GLY n 2 361 ILE n 2 362 ARG n 2 363 ASN n 2 364 LYS n 2 365 CYS n 2 366 LYS n 2 367 MET n 2 368 ASN n 2 369 LEU n 2 370 GLN n 2 371 ASP n 2 372 ASN n 2 373 ASN n 2 374 GLY n 2 375 ASN n 2 376 ASP n 2 377 ILE n 2 378 GLY n 2 379 PHE n 2 380 ILE n 2 381 GLY n 2 382 PHE n 2 383 HIS n 2 384 LEU n 2 385 TYR n 2 386 ASP n 2 387 ASN n 2 388 ILE n 2 389 ALA n 2 390 LYS n 2 391 LEU n 2 392 VAL n 2 393 ALA n 2 394 SER n 2 395 ASN n 2 396 TRP n 2 397 TYR n 2 398 ASN n 2 399 ARG n 2 400 GLN n 2 401 VAL n 2 402 GLY n 2 403 LYS n 2 404 ALA n 2 405 SER n 2 406 ARG n 2 407 THR n 2 408 PHE n 2 409 GLY n 2 410 CYS n 2 411 SER n 2 412 TRP n 2 413 GLU n 2 414 PHE n 2 415 ILE n 2 416 PRO n 2 417 VAL n 2 418 ASP n 2 419 ASP n 2 420 GLY n 2 421 TRP n 2 422 GLY n 2 423 GLU n 2 424 SER n 2 425 SER n 2 426 LEU n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _entity_src_gen.pdbx_gene_src_variant _entity_src_gen.pdbx_gene_src_cell_line _entity_src_gen.pdbx_gene_src_atcc _entity_src_gen.pdbx_gene_src_organ _entity_src_gen.pdbx_gene_src_organelle _entity_src_gen.pdbx_gene_src_cell _entity_src_gen.pdbx_gene_src_cellular_location _entity_src_gen.host_org_common_name _entity_src_gen.pdbx_host_org_scientific_name _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _entity_src_gen.host_org_genus _entity_src_gen.pdbx_host_org_gene _entity_src_gen.pdbx_host_org_organ _entity_src_gen.host_org_species _entity_src_gen.pdbx_host_org_tissue _entity_src_gen.pdbx_host_org_tissue_fraction _entity_src_gen.pdbx_host_org_strain _entity_src_gen.pdbx_host_org_variant _entity_src_gen.pdbx_host_org_cell_line _entity_src_gen.pdbx_host_org_atcc _entity_src_gen.pdbx_host_org_culture_collection _entity_src_gen.pdbx_host_org_cell _entity_src_gen.pdbx_host_org_organelle _entity_src_gen.pdbx_host_org_cellular_location _entity_src_gen.pdbx_host_org_vector_type _entity_src_gen.pdbx_host_org_vector _entity_src_gen.host_org_details _entity_src_gen.expression_system_id _entity_src_gen.plasmid_name _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample 'Biological sequence' 1 108 human ? SV2A ? ? ? ? ? ? 'Homo sapiens' 9606 ? ? ? ? ? ? ? ? 'Spodoptera frugiperda' 7108 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 1 sample 'Biological sequence' 1 426 ? ? ? ? ? ? ? ? ? 'Clostridium botulinum' 1491 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 3 'DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROH' 'Glycam Condensed Sequence' GMML 1.0 2 3 'WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1' WURCS PDB2Glycan 1.1.0 3 3 '[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}' LINUCS PDB-CARE ? # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.value_order _pdbx_entity_branch_link.details 1 3 2 NAG C1 O1 1 NAG O4 HO4 sing ? 2 3 3 FUC C1 O1 1 NAG O6 HO6 sing ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 FUC 'L-saccharide, alpha linking' . alpha-L-fucopyranose 'alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose' 'C6 H12 O5' 164.156 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NAG 'D-saccharide, beta linking' . 2-acetamido-2-deoxy-beta-D-glucopyranose ;N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE ; 'C8 H15 N O6' 221.208 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier FUC 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 LFucpa FUC 'COMMON NAME' GMML 1.0 a-L-fucopyranose FUC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-L-Fucp FUC 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Fuc NAG 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpNAcb NAG 'COMMON NAME' GMML 1.0 N-acetyl-b-D-glucopyranosamine NAG 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-GlcpNAc NAG 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GlcNAc # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 TYR 1 480 480 TYR TYR A . n A 1 2 ALA 2 481 481 ALA ALA A . n A 1 3 SER 3 482 482 SER SER A . n A 1 4 ARG 4 483 483 ARG ARG A . n A 1 5 THR 5 484 484 THR THR A . n A 1 6 LYS 6 485 485 LYS LYS A . n A 1 7 VAL 7 486 486 VAL VAL A . n A 1 8 PHE 8 487 487 PHE PHE A . n A 1 9 PRO 9 488 488 PRO PRO A . n A 1 10 GLY 10 489 489 GLY GLY A . n A 1 11 GLU 11 490 490 GLU GLU A . n A 1 12 ARG 12 491 491 ARG ARG A . n A 1 13 VAL 13 492 492 VAL VAL A . n A 1 14 GLU 14 493 493 GLU GLU A . n A 1 15 HIS 15 494 494 HIS HIS A . n A 1 16 VAL 16 495 495 VAL VAL A . n A 1 17 THR 17 496 496 THR THR A . n A 1 18 PHE 18 497 497 PHE PHE A . n A 1 19 ASN 19 498 498 ASN ASN A . n A 1 20 PHE 20 499 499 PHE PHE A . n A 1 21 THR 21 500 500 THR THR A . n A 1 22 LEU 22 501 501 LEU LEU A . n A 1 23 GLU 23 502 502 GLU GLU A . n A 1 24 ASN 24 503 503 ASN ASN A . n A 1 25 GLN 25 504 504 GLN GLN A . n A 1 26 ILE 26 505 505 ILE ILE A . n A 1 27 HIS 27 506 506 HIS HIS A . n A 1 28 ARG 28 507 507 ARG ARG A . n A 1 29 GLY 29 508 508 GLY GLY A . n A 1 30 GLY 30 509 509 GLY GLY A . n A 1 31 GLN 31 510 510 GLN GLN A . n A 1 32 TYR 32 511 511 TYR TYR A . n A 1 33 PHE 33 512 512 PHE PHE A . n A 1 34 ASN 34 513 513 ASN ASN A . n A 1 35 ASP 35 514 514 ASP ASP A . n A 1 36 LYS 36 515 515 LYS LYS A . n A 1 37 PHE 37 516 516 PHE PHE A . n A 1 38 ILE 38 517 517 ILE ILE A . n A 1 39 GLY 39 518 518 GLY GLY A . n A 1 40 LEU 40 519 519 LEU LEU A . n A 1 41 ARG 41 520 520 ARG ARG A . n A 1 42 LEU 42 521 521 LEU LEU A . n A 1 43 LYS 43 522 522 LYS LYS A . n A 1 44 SER 44 523 523 SER SER A . n A 1 45 VAL 45 524 524 VAL VAL A . n A 1 46 SER 46 525 525 SER SER A . n A 1 47 PHE 47 526 526 PHE PHE A . n A 1 48 GLU 48 527 527 GLU GLU A . n A 1 49 ASP 49 528 528 ASP ASP A . n A 1 50 SER 50 529 529 SER SER A . n A 1 51 LEU 51 530 530 LEU LEU A . n A 1 52 PHE 52 531 531 PHE PHE A . n A 1 53 GLU 53 532 532 GLU GLU A . n A 1 54 GLU 54 533 533 GLU GLU A . n A 1 55 CYS 55 534 534 CYS CYS A . n A 1 56 TYR 56 535 535 TYR TYR A . n A 1 57 PHE 57 536 536 PHE PHE A . n A 1 58 GLU 58 537 537 GLU GLU A . n A 1 59 ASP 59 538 538 ASP ASP A . n A 1 60 VAL 60 539 539 VAL VAL A . n A 1 61 THR 61 540 540 THR THR A . n A 1 62 SER 62 541 541 SER SER A . n A 1 63 SER 63 542 542 SER SER A . n A 1 64 ASN 64 543 543 ASN ASN A . n A 1 65 THR 65 544 544 THR THR A . n A 1 66 PHE 66 545 545 PHE PHE A . n A 1 67 PHE 67 546 546 PHE PHE A . n A 1 68 ARG 68 547 547 ARG ARG A . n A 1 69 ASN 69 548 548 ASN ASN A . n A 1 70 CYS 70 549 549 CYS CYS A . n A 1 71 THR 71 550 550 THR THR A . n A 1 72 PHE 72 551 551 PHE PHE A . n A 1 73 ILE 73 552 552 ILE ILE A . n A 1 74 ASN 74 553 553 ASN ASN A . n A 1 75 THR 75 554 554 THR THR A . n A 1 76 VAL 76 555 555 VAL VAL A . n A 1 77 PHE 77 556 556 PHE PHE A . n A 1 78 TYR 78 557 557 TYR TYR A . n A 1 79 ASN 79 558 558 ASN ASN A . n A 1 80 THR 80 559 559 THR THR A . n A 1 81 ASP 81 560 560 ASP ASP A . n A 1 82 LEU 82 561 561 LEU LEU A . n A 1 83 PHE 83 562 562 PHE PHE A . n A 1 84 GLU 84 563 563 GLU GLU A . n A 1 85 TYR 85 564 564 TYR TYR A . n A 1 86 LYS 86 565 565 LYS LYS A . n A 1 87 PHE 87 566 566 PHE PHE A . n A 1 88 VAL 88 567 567 VAL VAL A . n A 1 89 ASN 89 568 568 ASN ASN A . n A 1 90 SER 90 569 569 SER SER A . n A 1 91 ARG 91 570 570 ARG ARG A . n A 1 92 LEU 92 571 571 LEU LEU A . n A 1 93 ILE 93 572 572 ILE ILE A . n A 1 94 ASN 94 573 573 ASN ASN A . n A 1 95 SER 95 574 574 SER SER A . n A 1 96 THR 96 575 575 THR THR A . n A 1 97 PHE 97 576 576 PHE PHE A . n A 1 98 LEU 98 577 577 LEU LEU A . n A 1 99 HIS 99 578 578 HIS HIS A . n A 1 100 ASN 100 579 579 ASN ASN A . n A 1 101 LYS 101 580 580 LYS LYS A . n A 1 102 GLU 102 581 581 GLU GLU A . n A 1 103 GLY 103 582 582 GLY GLY A . n A 1 104 CYS 104 583 583 CYS CYS A . n A 1 105 PRO 105 584 584 PRO PRO A . n A 1 106 LEU 106 585 585 LEU LEU A . n A 1 107 ASP 107 586 586 ASP ASP A . n A 1 108 VAL 108 587 587 VAL VAL A . n B 2 1 LYS 1 871 ? ? ? B . n B 2 2 ASN 2 872 ? ? ? B . n B 2 3 ILE 3 873 ? ? ? B . n B 2 4 VAL 4 874 ? ? ? B . n B 2 5 ASN 5 875 ? ? ? B . n B 2 6 THR 6 876 876 THR THR B . n B 2 7 SER 7 877 877 SER SER B . n B 2 8 ILE 8 878 878 ILE ILE B . n B 2 9 LEU 9 879 879 LEU LEU B . n B 2 10 SER 10 880 880 SER SER B . n B 2 11 ILE 11 881 881 ILE ILE B . n B 2 12 VAL 12 882 882 VAL VAL B . n B 2 13 TYR 13 883 883 TYR TYR B . n B 2 14 LYS 14 884 884 LYS LYS B . n B 2 15 LYS 15 885 885 LYS LYS B . n B 2 16 ASP 16 886 886 ASP ASP B . n B 2 17 ASP 17 887 887 ASP ASP B . n B 2 18 LEU 18 888 888 LEU LEU B . n B 2 19 ILE 19 889 889 ILE ILE B . n B 2 20 ASP 20 890 890 ASP ASP B . n B 2 21 LEU 21 891 891 LEU LEU B . n B 2 22 SER 22 892 892 SER SER B . n B 2 23 ARG 23 893 893 ARG ARG B . n B 2 24 TYR 24 894 894 TYR TYR B . n B 2 25 GLY 25 895 895 GLY GLY B . n B 2 26 ALA 26 896 896 ALA ALA B . n B 2 27 LYS 27 897 897 LYS LYS B . n B 2 28 ILE 28 898 898 ILE ILE B . n B 2 29 ASN 29 899 899 ASN ASN B . n B 2 30 ILE 30 900 900 ILE ILE B . n B 2 31 GLY 31 901 901 GLY GLY B . n B 2 32 ASP 32 902 902 ASP ASP B . n B 2 33 ARG 33 903 903 ARG ARG B . n B 2 34 VAL 34 904 904 VAL VAL B . n B 2 35 TYR 35 905 905 TYR TYR B . n B 2 36 TYR 36 906 906 TYR TYR B . n B 2 37 ASP 37 907 907 ASP ASP B . n B 2 38 SER 38 908 908 SER SER B . n B 2 39 ILE 39 909 909 ILE ILE B . n B 2 40 ASP 40 910 910 ASP ASP B . n B 2 41 LYS 41 911 911 LYS LYS B . n B 2 42 ASN 42 912 912 ASN ASN B . n B 2 43 GLN 43 913 913 GLN GLN B . n B 2 44 ILE 44 914 914 ILE ILE B . n B 2 45 LYS 45 915 915 LYS LYS B . n B 2 46 LEU 46 916 916 LEU LEU B . n B 2 47 ILE 47 917 917 ILE ILE B . n B 2 48 ASN 48 918 918 ASN ASN B . n B 2 49 LEU 49 919 919 LEU LEU B . n B 2 50 GLU 50 920 920 GLU GLU B . n B 2 51 SER 51 921 921 SER SER B . n B 2 52 SER 52 922 922 SER SER B . n B 2 53 THR 53 923 923 THR THR B . n B 2 54 ILE 54 924 924 ILE ILE B . n B 2 55 GLU 55 925 925 GLU GLU B . n B 2 56 VAL 56 926 926 VAL VAL B . n B 2 57 ILE 57 927 927 ILE ILE B . n B 2 58 LEU 58 928 928 LEU LEU B . n B 2 59 LYS 59 929 929 LYS LYS B . n B 2 60 ASN 60 930 930 ASN ASN B . n B 2 61 ALA 61 931 931 ALA ALA B . n B 2 62 ILE 62 932 932 ILE ILE B . n B 2 63 VAL 63 933 933 VAL VAL B . n B 2 64 TYR 64 934 934 TYR TYR B . n B 2 65 ASN 65 935 935 ASN ASN B . n B 2 66 SER 66 936 936 SER SER B . n B 2 67 MET 67 937 937 MET MET B . n B 2 68 TYR 68 938 938 TYR TYR B . n B 2 69 GLU 69 939 939 GLU GLU B . n B 2 70 ASN 70 940 940 ASN ASN B . n B 2 71 PHE 71 941 941 PHE PHE B . n B 2 72 SER 72 942 942 SER SER B . n B 2 73 THR 73 943 943 THR THR B . n B 2 74 SER 74 944 944 SER SER B . n B 2 75 PHE 75 945 945 PHE PHE B . n B 2 76 TRP 76 946 946 TRP TRP B . n B 2 77 ILE 77 947 947 ILE ILE B . n B 2 78 LYS 78 948 948 LYS LYS B . n B 2 79 ILE 79 949 949 ILE ILE B . n B 2 80 PRO 80 950 950 PRO PRO B . n B 2 81 LYS 81 951 951 LYS LYS B . n B 2 82 TYR 82 952 952 TYR TYR B . n B 2 83 PHE 83 953 953 PHE PHE B . n B 2 84 SER 84 954 954 SER SER B . n B 2 85 LYS 85 955 955 LYS LYS B . n B 2 86 ILE 86 956 956 ILE ILE B . n B 2 87 ASN 87 957 957 ASN ASN B . n B 2 88 LEU 88 958 958 LEU LEU B . n B 2 89 ASN 89 959 959 ASN ASN B . n B 2 90 ASN 90 960 960 ASN ASN B . n B 2 91 GLU 91 961 961 GLU GLU B . n B 2 92 TYR 92 962 962 TYR TYR B . n B 2 93 THR 93 963 963 THR THR B . n B 2 94 ILE 94 964 964 ILE ILE B . n B 2 95 ILE 95 965 965 ILE ILE B . n B 2 96 ASN 96 966 966 ASN ASN B . n B 2 97 CYS 97 967 967 CYS CYS B . n B 2 98 ILE 98 968 968 ILE ILE B . n B 2 99 GLU 99 969 969 GLU GLU B . n B 2 100 ASN 100 970 970 ASN ASN B . n B 2 101 ASN 101 971 971 ASN ASN B . n B 2 102 SER 102 972 972 SER SER B . n B 2 103 GLY 103 973 973 GLY GLY B . n B 2 104 TRP 104 974 974 TRP TRP B . n B 2 105 LYS 105 975 975 LYS LYS B . n B 2 106 VAL 106 976 976 VAL VAL B . n B 2 107 SER 107 977 977 SER SER B . n B 2 108 LEU 108 978 978 LEU LEU B . n B 2 109 ASN 109 979 979 ASN ASN B . n B 2 110 TYR 110 980 980 TYR TYR B . n B 2 111 GLY 111 981 981 GLY GLY B . n B 2 112 GLU 112 982 982 GLU GLU B . n B 2 113 ILE 113 983 983 ILE ILE B . n B 2 114 ILE 114 984 984 ILE ILE B . n B 2 115 TRP 115 985 985 TRP TRP B . n B 2 116 THR 116 986 986 THR THR B . n B 2 117 LEU 117 987 987 LEU LEU B . n B 2 118 GLN 118 988 988 GLN GLN B . n B 2 119 ASP 119 989 989 ASP ASP B . n B 2 120 ASN 120 990 990 ASN ASN B . n B 2 121 LYS 121 991 991 LYS LYS B . n B 2 122 GLN 122 992 992 GLN GLN B . n B 2 123 ASN 123 993 993 ASN ASN B . n B 2 124 ILE 124 994 994 ILE ILE B . n B 2 125 GLN 125 995 995 GLN GLN B . n B 2 126 ARG 126 996 996 ARG ARG B . n B 2 127 VAL 127 997 997 VAL VAL B . n B 2 128 VAL 128 998 998 VAL VAL B . n B 2 129 PHE 129 999 999 PHE PHE B . n B 2 130 LYS 130 1000 1000 LYS LYS B . n B 2 131 TYR 131 1001 1001 TYR TYR B . n B 2 132 SER 132 1002 1002 SER SER B . n B 2 133 GLN 133 1003 1003 GLN GLN B . n B 2 134 MET 134 1004 1004 MET MET B . n B 2 135 VAL 135 1005 1005 VAL VAL B . n B 2 136 ASN 136 1006 1006 ASN ASN B . n B 2 137 ILE 137 1007 1007 ILE ILE B . n B 2 138 SER 138 1008 1008 SER SER B . n B 2 139 ASP 139 1009 1009 ASP ASP B . n B 2 140 TYR 140 1010 1010 TYR TYR B . n B 2 141 ILE 141 1011 1011 ILE ILE B . n B 2 142 ASN 142 1012 1012 ASN ASN B . n B 2 143 ARG 143 1013 1013 ARG ARG B . n B 2 144 TRP 144 1014 1014 TRP TRP B . n B 2 145 ILE 145 1015 1015 ILE ILE B . n B 2 146 PHE 146 1016 1016 PHE PHE B . n B 2 147 VAL 147 1017 1017 VAL VAL B . n B 2 148 THR 148 1018 1018 THR THR B . n B 2 149 ILE 149 1019 1019 ILE ILE B . n B 2 150 THR 150 1020 1020 THR THR B . n B 2 151 ASN 151 1021 1021 ASN ASN B . n B 2 152 ASN 152 1022 1022 ASN ASN B . n B 2 153 ARG 153 1023 1023 ARG ARG B . n B 2 154 LEU 154 1024 1024 LEU LEU B . n B 2 155 THR 155 1025 1025 THR THR B . n B 2 156 LYS 156 1026 1026 LYS LYS B . n B 2 157 SER 157 1027 1027 SER SER B . n B 2 158 LYS 158 1028 1028 LYS LYS B . n B 2 159 ILE 159 1029 1029 ILE ILE B . n B 2 160 TYR 160 1030 1030 TYR TYR B . n B 2 161 ILE 161 1031 1031 ILE ILE B . n B 2 162 ASN 162 1032 1032 ASN ASN B . n B 2 163 GLY 163 1033 1033 GLY GLY B . n B 2 164 ARG 164 1034 1034 ARG ARG B . n B 2 165 LEU 165 1035 1035 LEU LEU B . n B 2 166 ILE 166 1036 1036 ILE ILE B . n B 2 167 ASP 167 1037 1037 ASP ASP B . n B 2 168 GLN 168 1038 1038 GLN GLN B . n B 2 169 LYS 169 1039 1039 LYS LYS B . n B 2 170 PRO 170 1040 1040 PRO PRO B . n B 2 171 ILE 171 1041 1041 ILE ILE B . n B 2 172 SER 172 1042 1042 SER SER B . n B 2 173 ASN 173 1043 1043 ASN ASN B . n B 2 174 LEU 174 1044 1044 LEU LEU B . n B 2 175 GLY 175 1045 1045 GLY GLY B . n B 2 176 ASN 176 1046 1046 ASN ASN B . n B 2 177 ILE 177 1047 1047 ILE ILE B . n B 2 178 HIS 178 1048 1048 HIS HIS B . n B 2 179 ALA 179 1049 1049 ALA ALA B . n B 2 180 SER 180 1050 1050 SER SER B . n B 2 181 ASN 181 1051 1051 ASN ASN B . n B 2 182 LYS 182 1052 1052 LYS LYS B . n B 2 183 ILE 183 1053 1053 ILE ILE B . n B 2 184 MET 184 1054 1054 MET MET B . n B 2 185 PHE 185 1055 1055 PHE PHE B . n B 2 186 LYS 186 1056 1056 LYS LYS B . n B 2 187 LEU 187 1057 1057 LEU LEU B . n B 2 188 ASP 188 1058 1058 ASP ASP B . n B 2 189 GLY 189 1059 1059 GLY GLY B . n B 2 190 CYS 190 1060 1060 CYS CYS B . n B 2 191 ARG 191 1061 1061 ARG ARG B . n B 2 192 ASP 192 1062 1062 ASP ASP B . n B 2 193 PRO 193 1063 1063 PRO PRO B . n B 2 194 ARG 194 1064 1064 ARG ARG B . n B 2 195 ARG 195 1065 1065 ARG ARG B . n B 2 196 TYR 196 1066 1066 TYR TYR B . n B 2 197 ILE 197 1067 1067 ILE ILE B . n B 2 198 MET 198 1068 1068 MET MET B . n B 2 199 ILE 199 1069 1069 ILE ILE B . n B 2 200 LYS 200 1070 1070 LYS LYS B . n B 2 201 TYR 201 1071 1071 TYR TYR B . n B 2 202 PHE 202 1072 1072 PHE PHE B . n B 2 203 ASN 203 1073 1073 ASN ASN B . n B 2 204 LEU 204 1074 1074 LEU LEU B . n B 2 205 PHE 205 1075 1075 PHE PHE B . n B 2 206 ASP 206 1076 1076 ASP ASP B . n B 2 207 LYS 207 1077 1077 LYS LYS B . n B 2 208 GLU 208 1078 1078 GLU GLU B . n B 2 209 LEU 209 1079 1079 LEU LEU B . n B 2 210 ASN 210 1080 1080 ASN ASN B . n B 2 211 GLU 211 1081 1081 GLU GLU B . n B 2 212 LYS 212 1082 1082 LYS LYS B . n B 2 213 GLU 213 1083 1083 GLU GLU B . n B 2 214 ILE 214 1084 1084 ILE ILE B . n B 2 215 LYS 215 1085 1085 LYS LYS B . n B 2 216 ASP 216 1086 1086 ASP ASP B . n B 2 217 LEU 217 1087 1087 LEU LEU B . n B 2 218 TYR 218 1088 1088 TYR TYR B . n B 2 219 ASP 219 1089 1089 ASP ASP B . n B 2 220 SER 220 1090 1090 SER SER B . n B 2 221 GLN 221 1091 1091 GLN GLN B . n B 2 222 SER 222 1092 1092 SER SER B . n B 2 223 ASN 223 1093 1093 ASN ASN B . n B 2 224 SER 224 1094 1094 SER SER B . n B 2 225 GLY 225 1095 1095 GLY GLY B . n B 2 226 ILE 226 1096 1096 ILE ILE B . n B 2 227 LEU 227 1097 1097 LEU LEU B . n B 2 228 LYS 228 1098 1098 LYS LYS B . n B 2 229 ASP 229 1099 1099 ASP ASP B . n B 2 230 PHE 230 1100 1100 PHE PHE B . n B 2 231 TRP 231 1101 1101 TRP TRP B . n B 2 232 GLY 232 1102 1102 GLY GLY B . n B 2 233 ASN 233 1103 1103 ASN ASN B . n B 2 234 TYR 234 1104 1104 TYR TYR B . n B 2 235 LEU 235 1105 1105 LEU LEU B . n B 2 236 GLN 236 1106 1106 GLN GLN B . n B 2 237 TYR 237 1107 1107 TYR TYR B . n B 2 238 ASP 238 1108 1108 ASP ASP B . n B 2 239 LYS 239 1109 1109 LYS LYS B . n B 2 240 PRO 240 1110 1110 PRO PRO B . n B 2 241 TYR 241 1111 1111 TYR TYR B . n B 2 242 TYR 242 1112 1112 TYR TYR B . n B 2 243 MET 243 1113 1113 MET MET B . n B 2 244 LEU 244 1114 1114 LEU LEU B . n B 2 245 ASN 245 1115 1115 ASN ASN B . n B 2 246 LEU 246 1116 1116 LEU LEU B . n B 2 247 PHE 247 1117 1117 PHE PHE B . n B 2 248 ASP 248 1118 1118 ASP ASP B . n B 2 249 PRO 249 1119 1119 PRO PRO B . n B 2 250 ASN 250 1120 1120 ASN ASN B . n B 2 251 LYS 251 1121 1121 LYS LYS B . n B 2 252 TYR 252 1122 1122 TYR TYR B . n B 2 253 VAL 253 1123 1123 VAL VAL B . n B 2 254 ASP 254 1124 1124 ASP ASP B . n B 2 255 VAL 255 1125 1125 VAL VAL B . n B 2 256 ASN 256 1126 1126 ASN ASN B . n B 2 257 ASN 257 1127 1127 ASN ASN B . n B 2 258 ILE 258 1128 1128 ILE ILE B . n B 2 259 GLY 259 1129 1129 GLY GLY B . n B 2 260 ILE 260 1130 1130 ILE ILE B . n B 2 261 ARG 261 1131 1131 ARG ARG B . n B 2 262 GLY 262 1132 1132 GLY GLY B . n B 2 263 TYR 263 1133 1133 TYR TYR B . n B 2 264 MET 264 1134 1134 MET MET B . n B 2 265 TYR 265 1135 1135 TYR TYR B . n B 2 266 LEU 266 1136 1136 LEU LEU B . n B 2 267 LYS 267 1137 1137 LYS LYS B . n B 2 268 GLY 268 1138 1138 GLY GLY B . n B 2 269 PRO 269 1139 1139 PRO PRO B . n B 2 270 ARG 270 1140 1140 ARG ARG B . n B 2 271 GLY 271 1141 1141 GLY GLY B . n B 2 272 SER 272 1142 1142 SER SER B . n B 2 273 VAL 273 1143 1143 VAL VAL B . n B 2 274 VAL 274 1144 1144 VAL VAL B . n B 2 275 THR 275 1145 1145 THR THR B . n B 2 276 THR 276 1146 1146 THR THR B . n B 2 277 ASN 277 1147 1147 ASN ASN B . n B 2 278 ILE 278 1148 1148 ILE ILE B . n B 2 279 TYR 279 1149 1149 TYR TYR B . n B 2 280 LEU 280 1150 1150 LEU LEU B . n B 2 281 ASN 281 1151 1151 ASN ASN B . n B 2 282 SER 282 1152 1152 SER SER B . n B 2 283 THR 283 1153 1153 THR THR B . n B 2 284 LEU 284 1154 1154 LEU LEU B . n B 2 285 TYR 285 1155 1155 TYR TYR B . n B 2 286 GLU 286 1156 1156 GLU GLU B . n B 2 287 GLY 287 1157 1157 GLY GLY B . n B 2 288 THR 288 1158 1158 THR THR B . n B 2 289 LYS 289 1159 1159 LYS LYS B . n B 2 290 PHE 290 1160 1160 PHE PHE B . n B 2 291 ILE 291 1161 1161 ILE ILE B . n B 2 292 ILE 292 1162 1162 ILE ILE B . n B 2 293 LYS 293 1163 1163 LYS LYS B . n B 2 294 LYS 294 1164 1164 LYS LYS B . n B 2 295 TYR 295 1165 1165 TYR TYR B . n B 2 296 ALA 296 1166 1166 ALA ALA B . n B 2 297 SER 297 1167 1167 SER SER B . n B 2 298 GLY 298 1168 1168 GLY GLY B . n B 2 299 ASN 299 1169 1169 ASN ASN B . n B 2 300 GLU 300 1170 1170 GLU GLU B . n B 2 301 ASP 301 1171 1171 ASP ASP B . n B 2 302 ASN 302 1172 1172 ASN ASN B . n B 2 303 ILE 303 1173 1173 ILE ILE B . n B 2 304 VAL 304 1174 1174 VAL VAL B . n B 2 305 ARG 305 1175 1175 ARG ARG B . n B 2 306 ASN 306 1176 1176 ASN ASN B . n B 2 307 ASN 307 1177 1177 ASN ASN B . n B 2 308 ASP 308 1178 1178 ASP ASP B . n B 2 309 ARG 309 1179 1179 ARG ARG B . n B 2 310 VAL 310 1180 1180 VAL VAL B . n B 2 311 TYR 311 1181 1181 TYR TYR B . n B 2 312 ILE 312 1182 1182 ILE ILE B . n B 2 313 ASN 313 1183 1183 ASN ASN B . n B 2 314 VAL 314 1184 1184 VAL VAL B . n B 2 315 VAL 315 1185 1185 VAL VAL B . n B 2 316 VAL 316 1186 1186 VAL VAL B . n B 2 317 LYS 317 1187 1187 LYS LYS B . n B 2 318 ASN 318 1188 1188 ASN ASN B . n B 2 319 LYS 319 1189 1189 LYS LYS B . n B 2 320 GLU 320 1190 1190 GLU GLU B . n B 2 321 TYR 321 1191 1191 TYR TYR B . n B 2 322 ARG 322 1192 1192 ARG ARG B . n B 2 323 LEU 323 1193 1193 LEU LEU B . n B 2 324 ALA 324 1194 1194 ALA ALA B . n B 2 325 THR 325 1195 1195 THR THR B . n B 2 326 ASN 326 1196 1196 ASN ASN B . n B 2 327 ALA 327 1197 1197 ALA ALA B . n B 2 328 SER 328 1198 1198 SER SER B . n B 2 329 GLN 329 1199 1199 GLN GLN B . n B 2 330 ALA 330 1200 1200 ALA ALA B . n B 2 331 GLY 331 1201 1201 GLY GLY B . n B 2 332 VAL 332 1202 1202 VAL VAL B . n B 2 333 GLU 333 1203 1203 GLU GLU B . n B 2 334 LYS 334 1204 1204 LYS LYS B . n B 2 335 ILE 335 1205 1205 ILE ILE B . n B 2 336 LEU 336 1206 1206 LEU LEU B . n B 2 337 SER 337 1207 1207 SER SER B . n B 2 338 ALA 338 1208 1208 ALA ALA B . n B 2 339 LEU 339 1209 1209 LEU LEU B . n B 2 340 GLU 340 1210 1210 GLU GLU B . n B 2 341 ILE 341 1211 1211 ILE ILE B . n B 2 342 PRO 342 1212 1212 PRO PRO B . n B 2 343 ASP 343 1213 1213 ASP ASP B . n B 2 344 VAL 344 1214 1214 VAL VAL B . n B 2 345 GLY 345 1215 1215 GLY GLY B . n B 2 346 ASN 346 1216 1216 ASN ASN B . n B 2 347 LEU 347 1217 1217 LEU LEU B . n B 2 348 SER 348 1218 1218 SER SER B . n B 2 349 GLN 349 1219 1219 GLN GLN B . n B 2 350 VAL 350 1220 1220 VAL VAL B . n B 2 351 VAL 351 1221 1221 VAL VAL B . n B 2 352 VAL 352 1222 1222 VAL VAL B . n B 2 353 MET 353 1223 1223 MET MET B . n B 2 354 LYS 354 1224 1224 LYS LYS B . n B 2 355 SER 355 1225 1225 SER SER B . n B 2 356 LYS 356 1226 1226 LYS LYS B . n B 2 357 ASP 357 1227 1227 ASP ASP B . n B 2 358 ASP 358 1228 1228 ASP ASP B . n B 2 359 GLN 359 1229 1229 GLN GLN B . n B 2 360 GLY 360 1230 1230 GLY GLY B . n B 2 361 ILE 361 1231 1231 ILE ILE B . n B 2 362 ARG 362 1232 1232 ARG ARG B . n B 2 363 ASN 363 1233 1233 ASN ASN B . n B 2 364 LYS 364 1234 1234 LYS LYS B . n B 2 365 CYS 365 1235 1235 CYS CYS B . n B 2 366 LYS 366 1236 1236 LYS LYS B . n B 2 367 MET 367 1237 1237 MET MET B . n B 2 368 ASN 368 1238 1238 ASN ASN B . n B 2 369 LEU 369 1239 1239 LEU LEU B . n B 2 370 GLN 370 1240 1240 GLN GLN B . n B 2 371 ASP 371 1241 1241 ASP ASP B . n B 2 372 ASN 372 1242 1242 ASN ASN B . n B 2 373 ASN 373 1243 1243 ASN ASN B . n B 2 374 GLY 374 1244 1244 GLY GLY B . n B 2 375 ASN 375 1245 1245 ASN ASN B . n B 2 376 ASP 376 1246 1246 ASP ASP B . n B 2 377 ILE 377 1247 1247 ILE ILE B . n B 2 378 GLY 378 1248 1248 GLY GLY B . n B 2 379 PHE 379 1249 1249 PHE PHE B . n B 2 380 ILE 380 1250 1250 ILE ILE B . n B 2 381 GLY 381 1251 1251 GLY GLY B . n B 2 382 PHE 382 1252 1252 PHE PHE B . n B 2 383 HIS 383 1253 1253 HIS HIS B . n B 2 384 LEU 384 1254 1254 LEU LEU B . n B 2 385 TYR 385 1255 1255 TYR TYR B . n B 2 386 ASP 386 1256 1256 ASP ASP B . n B 2 387 ASN 387 1257 1257 ASN ASN B . n B 2 388 ILE 388 1258 1258 ILE ILE B . n B 2 389 ALA 389 1259 1259 ALA ALA B . n B 2 390 LYS 390 1260 1260 LYS LYS B . n B 2 391 LEU 391 1261 1261 LEU LEU B . n B 2 392 VAL 392 1262 1262 VAL VAL B . n B 2 393 ALA 393 1263 1263 ALA ALA B . n B 2 394 SER 394 1264 1264 SER SER B . n B 2 395 ASN 395 1265 1265 ASN ASN B . n B 2 396 TRP 396 1266 1266 TRP TRP B . n B 2 397 TYR 397 1267 1267 TYR TYR B . n B 2 398 ASN 398 1268 1268 ASN ASN B . n B 2 399 ARG 399 1269 1269 ARG ARG B . n B 2 400 GLN 400 1270 1270 GLN GLN B . n B 2 401 VAL 401 1271 1271 VAL VAL B . n B 2 402 GLY 402 1272 1272 GLY GLY B . n B 2 403 LYS 403 1273 1273 LYS LYS B . n B 2 404 ALA 404 1274 1274 ALA ALA B . n B 2 405 SER 405 1275 1275 SER SER B . n B 2 406 ARG 406 1276 1276 ARG ARG B . n B 2 407 THR 407 1277 1277 THR THR B . n B 2 408 PHE 408 1278 1278 PHE PHE B . n B 2 409 GLY 409 1279 1279 GLY GLY B . n B 2 410 CYS 410 1280 1280 CYS CYS B . n B 2 411 SER 411 1281 1281 SER SER B . n B 2 412 TRP 412 1282 1282 TRP TRP B . n B 2 413 GLU 413 1283 1283 GLU GLU B . n B 2 414 PHE 414 1284 1284 PHE PHE B . n B 2 415 ILE 415 1285 1285 ILE ILE B . n B 2 416 PRO 416 1286 1286 PRO PRO B . n B 2 417 VAL 417 1287 1287 VAL VAL B . n B 2 418 ASP 418 1288 1288 ASP ASP B . n B 2 419 ASP 419 1289 1289 ASP ASP B . n B 2 420 GLY 420 1290 1290 GLY GLY B . n B 2 421 TRP 421 1291 1291 TRP TRP B . n B 2 422 GLY 422 1292 1292 GLY GLY B . n B 2 423 GLU 423 1293 1293 GLU GLU B . n B 2 424 SER 424 1294 1294 SER SER B . n B 2 425 SER 425 1295 1295 SER SER B . n B 2 426 LEU 426 1296 ? ? ? B . n # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero C 3 NAG 1 E NAG 1 A NAG 902 n C 3 NAG 2 E NAG 2 A NAG 903 n C 3 FUC 3 E FUC 3 A FUC 904 n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 NAG 1 601 900 NAG NAG A . E 4 NAG 1 602 901 NAG NAG A . # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 8JLE _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8JLE _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8JLE _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 125.554 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.824 _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8JLE _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.82 _refine.ls_d_res_low 96.28 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 78964 _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 100.00 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.36618 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.36618 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'PARAMETERS FOR MASK CACLULATION' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.277 _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B 8.220 _refine.overall_SU_ML 0.157 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id 1 _refine_hist.details ? _refine_hist.d_res_high . _refine_hist.d_res_low . _refine_hist.number_atoms_solvent ? _refine_hist.number_atoms_total 4408 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein ? _refine_hist.pdbx_number_atoms_nucleic_acid ? _refine_hist.pdbx_number_atoms_ligand ? _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.010 0.011 4506 ? r_bond_refined_d ? ? 'ELECTRON MICROSCOPY' ? 0.000 0.016 4031 ? r_bond_other_d ? ? 'ELECTRON MICROSCOPY' ? 1.414 1.646 6096 ? r_angle_refined_deg ? ? 'ELECTRON MICROSCOPY' ? 0.456 1.563 9409 ? r_angle_other_deg ? ? 'ELECTRON MICROSCOPY' ? 5.714 5.000 526 ? r_dihedral_angle_1_deg ? ? 'ELECTRON MICROSCOPY' ? 4.223 5.000 23 ? r_dihedral_angle_2_deg ? ? 'ELECTRON MICROSCOPY' ? 13.714 10.000 794 ? r_dihedral_angle_3_deg ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'ELECTRON MICROSCOPY' ? 0.068 0.200 670 ? r_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.008 0.020 5062 ? r_gen_planes_refined ? ? 'ELECTRON MICROSCOPY' ? 0.001 0.020 935 ? r_gen_planes_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? 14.343 11.752 2110 ? r_mcbond_it ? ? 'ELECTRON MICROSCOPY' ? 14.341 11.752 2110 ? r_mcbond_other ? ? 'ELECTRON MICROSCOPY' ? 21.087 17.681 2634 ? r_mcangle_it ? ? 'ELECTRON MICROSCOPY' ? 21.084 17.683 2635 ? r_mcangle_other ? ? 'ELECTRON MICROSCOPY' ? 16.605 13.586 2396 ? r_scbond_it ? ? 'ELECTRON MICROSCOPY' ? 16.602 13.587 2397 ? r_scbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scangle_it ? ? 'ELECTRON MICROSCOPY' ? 25.969 19.588 3463 ? r_scangle_other ? ? 'ELECTRON MICROSCOPY' ? 39.759 ? 18112 ? r_long_range_B_refined ? ? 'ELECTRON MICROSCOPY' ? 39.758 ? 18113 ? r_long_range_B_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_rigid_bond_restr ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_free ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_ls_shell.d_res_high 2.820 _refine_ls_shell.d_res_low 2.894 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 0 _refine_ls_shell.number_reflns_R_work 5773 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 1.336 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? _refine_ls_shell.R_factor_R_free 0.000 # _struct.entry_id 8JLE _struct.title 'Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the SV2A-levetiracetam-BoNT/A2 Hc complex' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8JLE _struct_keywords.text 'Synaptic vesicle, epilepsy, TRANSPORT PROTEIN' _struct_keywords.pdbx_keywords 'TRANSPORT PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 UNP SV2A_HUMAN Q7L0J3 ? 1 ;YASRTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSSNTFFRNCTFINTVFYNT DLFEYKFVNSRLINSTFLHNKEGCPLDV ; 480 2 UNP D2KCK3_CLOBO D2KCK3 ? 2 ;KNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKNAIVYNSMYENFSTSFWIKIP KYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDNKQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIY INGRLIDQKPISNLGNIHASNKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKP YYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNEDNIVRNNDRVYINVVVKNKE YRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQGIRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQ VGKASRTFGCSWEFIPVDDGWGESSL ; 871 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 8JLE A 1 ? 108 ? Q7L0J3 480 ? 587 ? 480 587 2 2 8JLE B 1 ? 426 ? D2KCK3 871 ? 1296 ? 871 1296 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'electron microscopy' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 PHE A 83 ? TYR A 85 ? PHE A 562 TYR A 564 5 ? 3 HELX_P HELX_P2 AA2 LYS B 59 ? VAL B 63 ? LYS B 929 VAL B 933 5 ? 5 HELX_P HELX_P3 AA3 SER B 84 ? LEU B 88 ? SER B 954 LEU B 958 5 ? 5 HELX_P HELX_P4 AA4 ASN B 210 ? SER B 222 ? ASN B 1080 SER B 1092 1 ? 13 HELX_P HELX_P5 AA5 GLU B 340 ? GLY B 345 ? GLU B 1210 GLY B 1215 5 ? 6 HELX_P HELX_P6 AA6 ASN B 395 ? LYS B 403 ? ASN B 1265 LYS B 1273 1 ? 9 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A ASN 19 ND2 ? ? ? 1_555 D NAG . C1 ? ? A ASN 498 A NAG 601 1_555 ? ? ? ? ? ? ? 1.683 ? N-Glycosylation covale2 covale one ? A ASN 69 ND2 ? ? ? 1_555 E NAG . C1 ? ? A ASN 548 A NAG 602 1_555 ? ? ? ? ? ? ? 1.661 ? N-Glycosylation covale3 covale one ? A ASN 94 ND2 ? ? ? 1_555 C NAG . C1 ? ? A ASN 573 E NAG 1 1_555 ? ? ? ? ? ? ? 1.493 ? N-Glycosylation covale4 covale both ? C NAG . O4 ? ? ? 1_555 C NAG . C1 ? ? E NAG 1 E NAG 2 1_555 ? ? ? ? ? ? ? 1.435 ? ? covale5 covale both ? C NAG . O6 ? ? ? 1_555 C FUC . C1 ? ? E NAG 1 E FUC 3 1_555 ? ? ? ? ? ? ? 1.421 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLY _struct_mon_prot_cis.label_seq_id 268 _struct_mon_prot_cis.label_asym_id B _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLY _struct_mon_prot_cis.auth_seq_id 1138 _struct_mon_prot_cis.auth_asym_id B _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 269 _struct_mon_prot_cis.pdbx_label_asym_id_2 B _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 1139 _struct_mon_prot_cis.pdbx_auth_asym_id_2 B _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -7.06 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 6 ? AA2 ? 9 ? AA3 ? 5 ? AA4 ? 7 ? AA5 ? 3 ? AA6 ? 4 ? AA7 ? 2 ? AA8 ? 2 ? AA9 ? 7 ? AB1 ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? parallel AA1 2 3 ? parallel AA1 4 5 ? parallel AA1 5 6 ? parallel AA2 1 2 ? parallel AA2 2 3 ? parallel AA2 3 4 ? parallel AA2 5 6 ? parallel AA2 6 7 ? parallel AA2 7 8 ? anti-parallel AA2 8 9 ? anti-parallel AA3 1 2 ? anti-parallel AA3 2 3 ? anti-parallel AA3 3 4 ? anti-parallel AA3 4 5 ? anti-parallel AA4 1 2 ? anti-parallel AA4 2 3 ? anti-parallel AA4 3 4 ? anti-parallel AA4 4 5 ? anti-parallel AA4 5 6 ? anti-parallel AA4 6 7 ? anti-parallel AA5 1 2 ? anti-parallel AA5 2 3 ? anti-parallel AA6 1 2 ? anti-parallel AA6 2 3 ? anti-parallel AA6 3 4 ? anti-parallel AA7 1 2 ? anti-parallel AA8 1 2 ? anti-parallel AA9 1 2 ? anti-parallel AA9 2 3 ? anti-parallel AA9 3 4 ? anti-parallel AA9 4 5 ? anti-parallel AA9 5 6 ? anti-parallel AA9 6 7 ? anti-parallel AB1 1 2 ? anti-parallel AB1 2 3 ? anti-parallel AB1 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 LYS A 6 ? VAL A 13 ? LYS A 485 VAL A 492 AA1 2 THR A 21 ? PHE A 33 ? THR A 500 PHE A 512 AA1 3 LYS A 36 ? GLU A 48 ? LYS A 515 GLU A 527 AA1 4 LEU A 51 ? GLU A 53 ? LEU A 530 GLU A 532 AA1 5 THR A 71 ? ILE A 73 ? THR A 550 ILE A 552 AA1 6 ARG A 91 ? ILE A 93 ? ARG A 570 ILE A 572 AA2 1 PHE A 87 ? VAL A 88 ? PHE A 566 VAL A 567 AA2 2 PHE A 66 ? ARG A 68 ? PHE A 545 ARG A 547 AA2 3 LYS A 36 ? GLU A 48 ? LYS A 515 GLU A 527 AA2 4 THR A 21 ? PHE A 33 ? THR A 500 PHE A 512 AA2 5 TYR A 56 ? SER A 63 ? TYR A 535 SER A 542 AA2 6 VAL A 76 ? THR A 80 ? VAL A 555 THR A 559 AA2 7 SER A 95 ? LEU A 98 ? SER A 574 LEU A 577 AA2 8 SER B 272 ? VAL B 274 ? SER B 1142 VAL B 1144 AA2 9 LEU B 280 ? SER B 282 ? LEU B 1150 SER B 1152 AA3 1 ASP B 17 ? ASP B 20 ? ASP B 887 ASP B 890 AA3 2 SER B 7 ? LYS B 14 ? SER B 877 LYS B 884 AA3 3 ILE B 197 ? PHE B 205 ? ILE B 1067 PHE B 1075 AA3 4 GLN B 43 ? LEU B 46 ? GLN B 913 LEU B 916 AA3 5 TYR B 35 ? TYR B 36 ? TYR B 905 TYR B 906 AA4 1 ASP B 17 ? ASP B 20 ? ASP B 887 ASP B 890 AA4 2 SER B 7 ? LYS B 14 ? SER B 877 LYS B 884 AA4 3 ILE B 197 ? PHE B 205 ? ILE B 1067 PHE B 1075 AA4 4 PHE B 71 ? LYS B 78 ? PHE B 941 LYS B 948 AA4 5 ILE B 145 ? ASN B 151 ? ILE B 1015 ASN B 1021 AA4 6 SER B 157 ? ILE B 161 ? SER B 1027 ILE B 1031 AA4 7 ARG B 164 ? LYS B 169 ? ARG B 1034 LYS B 1039 AA5 1 LYS B 27 ? ILE B 30 ? LYS B 897 ILE B 900 AA5 2 ILE B 54 ? ILE B 57 ? ILE B 924 ILE B 927 AA5 3 LYS B 182 ? PHE B 185 ? LYS B 1052 PHE B 1055 AA6 1 TYR B 92 ? ASN B 96 ? TYR B 962 ASN B 966 AA6 2 GLY B 103 ? ASN B 109 ? GLY B 973 ASN B 979 AA6 3 GLU B 112 ? GLN B 118 ? GLU B 982 GLN B 988 AA6 4 ILE B 124 ? LYS B 130 ? ILE B 994 LYS B 1000 AA7 1 TYR B 242 ? ASN B 245 ? TYR B 1112 ASN B 1115 AA7 2 TRP B 412 ? ILE B 415 ? TRP B 1282 ILE B 1285 AA8 1 TYR B 252 ? VAL B 255 ? TYR B 1122 VAL B 1125 AA8 2 MET B 264 ? LYS B 267 ? MET B 1134 LYS B 1137 AA9 1 LYS B 289 ? LYS B 294 ? LYS B 1159 LYS B 1164 AA9 2 ARG B 309 ? VAL B 316 ? ARG B 1179 VAL B 1186 AA9 3 VAL B 350 ? LYS B 356 ? VAL B 1220 LYS B 1226 AA9 4 ARG B 362 ? GLN B 370 ? ARG B 1232 GLN B 1240 AA9 5 ASP B 376 ? TYR B 385 ? ASP B 1246 TYR B 1255 AA9 6 ILE B 388 ? SER B 394 ? ILE B 1258 SER B 1264 AA9 7 LYS B 334 ? ILE B 335 ? LYS B 1204 ILE B 1205 AB1 1 LYS B 289 ? LYS B 294 ? LYS B 1159 LYS B 1164 AB1 2 ARG B 309 ? VAL B 316 ? ARG B 1179 VAL B 1186 AB1 3 LYS B 319 ? ALA B 324 ? LYS B 1189 ALA B 1194 AB1 4 SER B 337 ? LEU B 339 ? SER B 1207 LEU B 1209 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N GLY A 10 ? N GLY A 489 O ARG A 28 ? O ARG A 507 AA1 2 3 N HIS A 27 ? N HIS A 506 O GLU A 48 ? O GLU A 527 AA1 4 5 N PHE A 52 ? N PHE A 531 O THR A 71 ? O THR A 550 AA1 5 6 N PHE A 72 ? N PHE A 551 O ILE A 93 ? O ILE A 572 AA2 1 2 O VAL A 88 ? O VAL A 567 N PHE A 67 ? N PHE A 546 AA2 2 3 O PHE A 66 ? O PHE A 545 N PHE A 47 ? N PHE A 526 AA2 3 4 O GLU A 48 ? O GLU A 527 N HIS A 27 ? N HIS A 506 AA2 5 6 N PHE A 57 ? N PHE A 536 O VAL A 76 ? O VAL A 555 AA2 6 7 N PHE A 77 ? N PHE A 556 O THR A 96 ? O THR A 575 AA2 7 8 N SER A 95 ? N SER A 574 O VAL B 274 ? O VAL B 1144 AA2 8 9 N VAL B 273 ? N VAL B 1143 O ASN B 281 ? O ASN B 1151 AA3 1 2 O ILE B 19 ? O ILE B 889 N VAL B 12 ? N VAL B 882 AA3 2 3 N ILE B 8 ? N ILE B 878 O LEU B 204 ? O LEU B 1074 AA3 3 4 O ILE B 199 ? O ILE B 1069 N ILE B 44 ? N ILE B 914 AA3 4 5 O LYS B 45 ? O LYS B 915 N TYR B 35 ? N TYR B 905 AA4 1 2 O ILE B 19 ? O ILE B 889 N VAL B 12 ? N VAL B 882 AA4 2 3 N ILE B 8 ? N ILE B 878 O LEU B 204 ? O LEU B 1074 AA4 3 4 O LYS B 200 ? O LYS B 1070 N TRP B 76 ? N TRP B 946 AA4 4 5 N ILE B 77 ? N ILE B 947 O ILE B 145 ? O ILE B 1015 AA4 5 6 N THR B 150 ? N THR B 1020 O LYS B 158 ? O LYS B 1028 AA4 6 7 N ILE B 159 ? N ILE B 1029 O ASP B 167 ? O ASP B 1037 AA5 1 2 N LYS B 27 ? N LYS B 897 O ILE B 57 ? O ILE B 927 AA5 2 3 N VAL B 56 ? N VAL B 926 O ILE B 183 ? O ILE B 1053 AA6 1 2 N TYR B 92 ? N TYR B 962 O LEU B 108 ? O LEU B 978 AA6 2 3 N SER B 107 ? N SER B 977 O ILE B 114 ? O ILE B 984 AA6 3 4 N TRP B 115 ? N TRP B 985 O VAL B 127 ? O VAL B 997 AA7 1 2 N TYR B 242 ? N TYR B 1112 O ILE B 415 ? O ILE B 1285 AA8 1 2 N TYR B 252 ? N TYR B 1122 O LYS B 267 ? O LYS B 1137 AA9 1 2 N LYS B 293 ? N LYS B 1163 O TYR B 311 ? O TYR B 1181 AA9 2 3 N VAL B 310 ? N VAL B 1180 O VAL B 351 ? O VAL B 1221 AA9 3 4 N VAL B 350 ? N VAL B 1220 O GLN B 370 ? O GLN B 1240 AA9 4 5 N LEU B 369 ? N LEU B 1239 O GLY B 378 ? O GLY B 1248 AA9 5 6 N TYR B 385 ? N TYR B 1255 O ILE B 388 ? O ILE B 1258 AA9 6 7 O ALA B 393 ? O ALA B 1263 N LYS B 334 ? N LYS B 1204 AB1 1 2 N LYS B 293 ? N LYS B 1163 O TYR B 311 ? O TYR B 1181 AB1 2 3 N VAL B 316 ? N VAL B 1186 O LYS B 319 ? O LYS B 1189 AB1 3 4 N ALA B 324 ? N ALA B 1194 O SER B 337 ? O SER B 1207 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 ND2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ASN _pdbx_validate_close_contact.auth_seq_id_1 548 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O5 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 NAG _pdbx_validate_close_contact.auth_seq_id_2 602 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.97 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A ARG 547 ? ? CZ A ARG 547 ? ? NH2 A ARG 547 ? ? 116.77 120.30 -3.53 0.50 N 2 1 NE B ARG 1140 ? ? CZ B ARG 1140 ? ? NH1 B ARG 1140 ? ? 123.88 120.30 3.58 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 PHE A 497 ? ? -161.26 77.92 2 1 LYS B 884 ? ? -148.74 -159.27 3 1 LYS B 885 ? ? -69.09 92.79 4 1 ARG B 893 ? ? -84.33 47.65 5 1 PRO B 950 ? ? -59.15 178.07 6 1 TYR B 980 ? ? -49.31 109.71 7 1 TYR B 1071 ? ? 52.62 83.40 8 1 THR B 1145 ? ? -143.81 36.97 9 1 THR B 1146 ? ? 32.10 100.38 10 1 ASN B 1147 ? ? 83.19 -0.42 11 1 ASP B 1227 ? ? -78.48 -168.87 12 1 ASP B 1256 ? ? 36.45 58.69 # _pdbx_entry_details.entry_id 8JLE _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 8JLE _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 8JLE _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 2.82 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 646723 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details '20 mM Hepes (pH7.5), 150 mM NaCl, 0.001% LMNG, 0.0002% cholesterol hemisuccinate' _em_buffer.pH 7.5 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'SV2A in complex with BoNT/A2 Hc domain and anti-epileptic drug, levetiracetam' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1,2 # _em_imaging.entry_id 8JLE _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_min 800 _em_imaging.nominal_defocus_max 2000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.method ? _em_sample_support.film_material ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? _em_sample_support.details ? # _em_vitrification.entry_id 8JLE _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name ETHANE _em_vitrification.humidity 100 _em_vitrification.temp ? _em_vitrification.chamber_temperature 297 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 8JLE _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 B LYS 871 ? B LYS 1 2 1 Y 1 B ASN 872 ? B ASN 2 3 1 Y 1 B ILE 873 ? B ILE 3 4 1 Y 1 B VAL 874 ? B VAL 4 5 1 Y 1 B ASN 875 ? B ASN 5 6 1 Y 1 B LEU 1296 ? B LEU 426 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CYS N N N N 74 CYS CA C N R 75 CYS C C N N 76 CYS O O N N 77 CYS CB C N N 78 CYS SG S N N 79 CYS OXT O N N 80 CYS H H N N 81 CYS H2 H N N 82 CYS HA H N N 83 CYS HB2 H N N 84 CYS HB3 H N N 85 CYS HG H N N 86 CYS HXT H N N 87 FUC C1 C N R 88 FUC C2 C N S 89 FUC C3 C N R 90 FUC C4 C N S 91 FUC C5 C N S 92 FUC C6 C N N 93 FUC O1 O N N 94 FUC O2 O N N 95 FUC O3 O N N 96 FUC O4 O N N 97 FUC O5 O N N 98 FUC H1 H N N 99 FUC H2 H N N 100 FUC H3 H N N 101 FUC H4 H N N 102 FUC H5 H N N 103 FUC H61 H N N 104 FUC H62 H N N 105 FUC H63 H N N 106 FUC HO1 H N N 107 FUC HO2 H N N 108 FUC HO3 H N N 109 FUC HO4 H N N 110 GLN N N N N 111 GLN CA C N S 112 GLN C C N N 113 GLN O O N N 114 GLN CB C N N 115 GLN CG C N N 116 GLN CD C N N 117 GLN OE1 O N N 118 GLN NE2 N N N 119 GLN OXT O N N 120 GLN H H N N 121 GLN H2 H N N 122 GLN HA H N N 123 GLN HB2 H N N 124 GLN HB3 H N N 125 GLN HG2 H N N 126 GLN HG3 H N N 127 GLN HE21 H N N 128 GLN HE22 H N N 129 GLN HXT H N N 130 GLU N N N N 131 GLU CA C N S 132 GLU C C N N 133 GLU O O N N 134 GLU CB C N N 135 GLU CG C N N 136 GLU CD C N N 137 GLU OE1 O N N 138 GLU OE2 O N N 139 GLU OXT O N N 140 GLU H H N N 141 GLU H2 H N N 142 GLU HA H N N 143 GLU HB2 H N N 144 GLU HB3 H N N 145 GLU HG2 H N N 146 GLU HG3 H N N 147 GLU HE2 H N N 148 GLU HXT H N N 149 GLY N N N N 150 GLY CA C N N 151 GLY C C N N 152 GLY O O N N 153 GLY OXT O N N 154 GLY H H N N 155 GLY H2 H N N 156 GLY HA2 H N N 157 GLY HA3 H N N 158 GLY HXT H N N 159 HIS N N N N 160 HIS CA C N S 161 HIS C C N N 162 HIS O O N N 163 HIS CB C N N 164 HIS CG C Y N 165 HIS ND1 N Y N 166 HIS CD2 C Y N 167 HIS CE1 C Y N 168 HIS NE2 N Y N 169 HIS OXT O N N 170 HIS H H N N 171 HIS H2 H N N 172 HIS HA H N N 173 HIS HB2 H N N 174 HIS HB3 H N N 175 HIS HD1 H N N 176 HIS HD2 H N N 177 HIS HE1 H N N 178 HIS HE2 H N N 179 HIS HXT H N N 180 ILE N N N N 181 ILE CA C N S 182 ILE C C N N 183 ILE O O N N 184 ILE CB C N S 185 ILE CG1 C N N 186 ILE CG2 C N N 187 ILE CD1 C N N 188 ILE OXT O N N 189 ILE H H N N 190 ILE H2 H N N 191 ILE HA H N N 192 ILE HB H N N 193 ILE HG12 H N N 194 ILE HG13 H N N 195 ILE HG21 H N N 196 ILE HG22 H N N 197 ILE HG23 H N N 198 ILE HD11 H N N 199 ILE HD12 H N N 200 ILE HD13 H N N 201 ILE HXT H N N 202 LEU N N N N 203 LEU CA C N S 204 LEU C C N N 205 LEU O O N N 206 LEU CB C N N 207 LEU CG C N N 208 LEU CD1 C N N 209 LEU CD2 C N N 210 LEU OXT O N N 211 LEU H H N N 212 LEU H2 H N N 213 LEU HA H N N 214 LEU HB2 H N N 215 LEU HB3 H N N 216 LEU HG H N N 217 LEU HD11 H N N 218 LEU HD12 H N N 219 LEU HD13 H N N 220 LEU HD21 H N N 221 LEU HD22 H N N 222 LEU HD23 H N N 223 LEU HXT H N N 224 LYS N N N N 225 LYS CA C N S 226 LYS C C N N 227 LYS O O N N 228 LYS CB C N N 229 LYS CG C N N 230 LYS CD C N N 231 LYS CE C N N 232 LYS NZ N N N 233 LYS OXT O N N 234 LYS H H N N 235 LYS H2 H N N 236 LYS HA H N N 237 LYS HB2 H N N 238 LYS HB3 H N N 239 LYS HG2 H N N 240 LYS HG3 H N N 241 LYS HD2 H N N 242 LYS HD3 H N N 243 LYS HE2 H N N 244 LYS HE3 H N N 245 LYS HZ1 H N N 246 LYS HZ2 H N N 247 LYS HZ3 H N N 248 LYS HXT H N N 249 MET N N N N 250 MET CA C N S 251 MET C C N N 252 MET O O N N 253 MET CB C N N 254 MET CG C N N 255 MET SD S N N 256 MET CE C N N 257 MET OXT O N N 258 MET H H N N 259 MET H2 H N N 260 MET HA H N N 261 MET HB2 H N N 262 MET HB3 H N N 263 MET HG2 H N N 264 MET HG3 H N N 265 MET HE1 H N N 266 MET HE2 H N N 267 MET HE3 H N N 268 MET HXT H N N 269 NAG C1 C N R 270 NAG C2 C N R 271 NAG C3 C N R 272 NAG C4 C N S 273 NAG C5 C N R 274 NAG C6 C N N 275 NAG C7 C N N 276 NAG C8 C N N 277 NAG N2 N N N 278 NAG O1 O N N 279 NAG O3 O N N 280 NAG O4 O N N 281 NAG O5 O N N 282 NAG O6 O N N 283 NAG O7 O N N 284 NAG H1 H N N 285 NAG H2 H N N 286 NAG H3 H N N 287 NAG H4 H N N 288 NAG H5 H N N 289 NAG H61 H N N 290 NAG H62 H N N 291 NAG H81 H N N 292 NAG H82 H N N 293 NAG H83 H N N 294 NAG HN2 H N N 295 NAG HO1 H N N 296 NAG HO3 H N N 297 NAG HO4 H N N 298 NAG HO6 H N N 299 PHE N N N N 300 PHE CA C N S 301 PHE C C N N 302 PHE O O N N 303 PHE CB C N N 304 PHE CG C Y N 305 PHE CD1 C Y N 306 PHE CD2 C Y N 307 PHE CE1 C Y N 308 PHE CE2 C Y N 309 PHE CZ C Y N 310 PHE OXT O N N 311 PHE H H N N 312 PHE H2 H N N 313 PHE HA H N N 314 PHE HB2 H N N 315 PHE HB3 H N N 316 PHE HD1 H N N 317 PHE HD2 H N N 318 PHE HE1 H N N 319 PHE HE2 H N N 320 PHE HZ H N N 321 PHE HXT H N N 322 PRO N N N N 323 PRO CA C N S 324 PRO C C N N 325 PRO O O N N 326 PRO CB C N N 327 PRO CG C N N 328 PRO CD C N N 329 PRO OXT O N N 330 PRO H H N N 331 PRO HA H N N 332 PRO HB2 H N N 333 PRO HB3 H N N 334 PRO HG2 H N N 335 PRO HG3 H N N 336 PRO HD2 H N N 337 PRO HD3 H N N 338 PRO HXT H N N 339 SER N N N N 340 SER CA C N S 341 SER C C N N 342 SER O O N N 343 SER CB C N N 344 SER OG O N N 345 SER OXT O N N 346 SER H H N N 347 SER H2 H N N 348 SER HA H N N 349 SER HB2 H N N 350 SER HB3 H N N 351 SER HG H N N 352 SER HXT H N N 353 THR N N N N 354 THR CA C N S 355 THR C C N N 356 THR O O N N 357 THR CB C N R 358 THR OG1 O N N 359 THR CG2 C N N 360 THR OXT O N N 361 THR H H N N 362 THR H2 H N N 363 THR HA H N N 364 THR HB H N N 365 THR HG1 H N N 366 THR HG21 H N N 367 THR HG22 H N N 368 THR HG23 H N N 369 THR HXT H N N 370 TRP N N N N 371 TRP CA C N S 372 TRP C C N N 373 TRP O O N N 374 TRP CB C N N 375 TRP CG C Y N 376 TRP CD1 C Y N 377 TRP CD2 C Y N 378 TRP NE1 N Y N 379 TRP CE2 C Y N 380 TRP CE3 C Y N 381 TRP CZ2 C Y N 382 TRP CZ3 C Y N 383 TRP CH2 C Y N 384 TRP OXT O N N 385 TRP H H N N 386 TRP H2 H N N 387 TRP HA H N N 388 TRP HB2 H N N 389 TRP HB3 H N N 390 TRP HD1 H N N 391 TRP HE1 H N N 392 TRP HE3 H N N 393 TRP HZ2 H N N 394 TRP HZ3 H N N 395 TRP HH2 H N N 396 TRP HXT H N N 397 TYR N N N N 398 TYR CA C N S 399 TYR C C N N 400 TYR O O N N 401 TYR CB C N N 402 TYR CG C Y N 403 TYR CD1 C Y N 404 TYR CD2 C Y N 405 TYR CE1 C Y N 406 TYR CE2 C Y N 407 TYR CZ C Y N 408 TYR OH O N N 409 TYR OXT O N N 410 TYR H H N N 411 TYR H2 H N N 412 TYR HA H N N 413 TYR HB2 H N N 414 TYR HB3 H N N 415 TYR HD1 H N N 416 TYR HD2 H N N 417 TYR HE1 H N N 418 TYR HE2 H N N 419 TYR HH H N N 420 TYR HXT H N N 421 VAL N N N N 422 VAL CA C N S 423 VAL C C N N 424 VAL O O N N 425 VAL CB C N N 426 VAL CG1 C N N 427 VAL CG2 C N N 428 VAL OXT O N N 429 VAL H H N N 430 VAL H2 H N N 431 VAL HA H N N 432 VAL HB H N N 433 VAL HG11 H N N 434 VAL HG12 H N N 435 VAL HG13 H N N 436 VAL HG21 H N N 437 VAL HG22 H N N 438 VAL HG23 H N N 439 VAL HXT H N N 440 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 CYS N CA sing N N 70 CYS N H sing N N 71 CYS N H2 sing N N 72 CYS CA C sing N N 73 CYS CA CB sing N N 74 CYS CA HA sing N N 75 CYS C O doub N N 76 CYS C OXT sing N N 77 CYS CB SG sing N N 78 CYS CB HB2 sing N N 79 CYS CB HB3 sing N N 80 CYS SG HG sing N N 81 CYS OXT HXT sing N N 82 FUC C1 C2 sing N N 83 FUC C1 O1 sing N N 84 FUC C1 O5 sing N N 85 FUC C1 H1 sing N N 86 FUC C2 C3 sing N N 87 FUC C2 O2 sing N N 88 FUC C2 H2 sing N N 89 FUC C3 C4 sing N N 90 FUC C3 O3 sing N N 91 FUC C3 H3 sing N N 92 FUC C4 C5 sing N N 93 FUC C4 O4 sing N N 94 FUC C4 H4 sing N N 95 FUC C5 C6 sing N N 96 FUC C5 O5 sing N N 97 FUC C5 H5 sing N N 98 FUC C6 H61 sing N N 99 FUC C6 H62 sing N N 100 FUC C6 H63 sing N N 101 FUC O1 HO1 sing N N 102 FUC O2 HO2 sing N N 103 FUC O3 HO3 sing N N 104 FUC O4 HO4 sing N N 105 GLN N CA sing N N 106 GLN N H sing N N 107 GLN N H2 sing N N 108 GLN CA C sing N N 109 GLN CA CB sing N N 110 GLN CA HA sing N N 111 GLN C O doub N N 112 GLN C OXT sing N N 113 GLN CB CG sing N N 114 GLN CB HB2 sing N N 115 GLN CB HB3 sing N N 116 GLN CG CD sing N N 117 GLN CG HG2 sing N N 118 GLN CG HG3 sing N N 119 GLN CD OE1 doub N N 120 GLN CD NE2 sing N N 121 GLN NE2 HE21 sing N N 122 GLN NE2 HE22 sing N N 123 GLN OXT HXT sing N N 124 GLU N CA sing N N 125 GLU N H sing N N 126 GLU N H2 sing N N 127 GLU CA C sing N N 128 GLU CA CB sing N N 129 GLU CA HA sing N N 130 GLU C O doub N N 131 GLU C OXT sing N N 132 GLU CB CG sing N N 133 GLU CB HB2 sing N N 134 GLU CB HB3 sing N N 135 GLU CG CD sing N N 136 GLU CG HG2 sing N N 137 GLU CG HG3 sing N N 138 GLU CD OE1 doub N N 139 GLU CD OE2 sing N N 140 GLU OE2 HE2 sing N N 141 GLU OXT HXT sing N N 142 GLY N CA sing N N 143 GLY N H sing N N 144 GLY N H2 sing N N 145 GLY CA C sing N N 146 GLY CA HA2 sing N N 147 GLY CA HA3 sing N N 148 GLY C O doub N N 149 GLY C OXT sing N N 150 GLY OXT HXT sing N N 151 HIS N CA sing N N 152 HIS N H sing N N 153 HIS N H2 sing N N 154 HIS CA C sing N N 155 HIS CA CB sing N N 156 HIS CA HA sing N N 157 HIS C O doub N N 158 HIS C OXT sing N N 159 HIS CB CG sing N N 160 HIS CB HB2 sing N N 161 HIS CB HB3 sing N N 162 HIS CG ND1 sing Y N 163 HIS CG CD2 doub Y N 164 HIS ND1 CE1 doub Y N 165 HIS ND1 HD1 sing N N 166 HIS CD2 NE2 sing Y N 167 HIS CD2 HD2 sing N N 168 HIS CE1 NE2 sing Y N 169 HIS CE1 HE1 sing N N 170 HIS NE2 HE2 sing N N 171 HIS OXT HXT sing N N 172 ILE N CA sing N N 173 ILE N H sing N N 174 ILE N H2 sing N N 175 ILE CA C sing N N 176 ILE CA CB sing N N 177 ILE CA HA sing N N 178 ILE C O doub N N 179 ILE C OXT sing N N 180 ILE CB CG1 sing N N 181 ILE CB CG2 sing N N 182 ILE CB HB sing N N 183 ILE CG1 CD1 sing N N 184 ILE CG1 HG12 sing N N 185 ILE CG1 HG13 sing N N 186 ILE CG2 HG21 sing N N 187 ILE CG2 HG22 sing N N 188 ILE CG2 HG23 sing N N 189 ILE CD1 HD11 sing N N 190 ILE CD1 HD12 sing N N 191 ILE CD1 HD13 sing N N 192 ILE OXT HXT sing N N 193 LEU N CA sing N N 194 LEU N H sing N N 195 LEU N H2 sing N N 196 LEU CA C sing N N 197 LEU CA CB sing N N 198 LEU CA HA sing N N 199 LEU C O doub N N 200 LEU C OXT sing N N 201 LEU CB CG sing N N 202 LEU CB HB2 sing N N 203 LEU CB HB3 sing N N 204 LEU CG CD1 sing N N 205 LEU CG CD2 sing N N 206 LEU CG HG sing N N 207 LEU CD1 HD11 sing N N 208 LEU CD1 HD12 sing N N 209 LEU CD1 HD13 sing N N 210 LEU CD2 HD21 sing N N 211 LEU CD2 HD22 sing N N 212 LEU CD2 HD23 sing N N 213 LEU OXT HXT sing N N 214 LYS N CA sing N N 215 LYS N H sing N N 216 LYS N H2 sing N N 217 LYS CA C sing N N 218 LYS CA CB sing N N 219 LYS CA HA sing N N 220 LYS C O doub N N 221 LYS C OXT sing N N 222 LYS CB CG sing N N 223 LYS CB HB2 sing N N 224 LYS CB HB3 sing N N 225 LYS CG CD sing N N 226 LYS CG HG2 sing N N 227 LYS CG HG3 sing N N 228 LYS CD CE sing N N 229 LYS CD HD2 sing N N 230 LYS CD HD3 sing N N 231 LYS CE NZ sing N N 232 LYS CE HE2 sing N N 233 LYS CE HE3 sing N N 234 LYS NZ HZ1 sing N N 235 LYS NZ HZ2 sing N N 236 LYS NZ HZ3 sing N N 237 LYS OXT HXT sing N N 238 MET N CA sing N N 239 MET N H sing N N 240 MET N H2 sing N N 241 MET CA C sing N N 242 MET CA CB sing N N 243 MET CA HA sing N N 244 MET C O doub N N 245 MET C OXT sing N N 246 MET CB CG sing N N 247 MET CB HB2 sing N N 248 MET CB HB3 sing N N 249 MET CG SD sing N N 250 MET CG HG2 sing N N 251 MET CG HG3 sing N N 252 MET SD CE sing N N 253 MET CE HE1 sing N N 254 MET CE HE2 sing N N 255 MET CE HE3 sing N N 256 MET OXT HXT sing N N 257 NAG C1 C2 sing N N 258 NAG C1 O1 sing N N 259 NAG C1 O5 sing N N 260 NAG C1 H1 sing N N 261 NAG C2 C3 sing N N 262 NAG C2 N2 sing N N 263 NAG C2 H2 sing N N 264 NAG C3 C4 sing N N 265 NAG C3 O3 sing N N 266 NAG C3 H3 sing N N 267 NAG C4 C5 sing N N 268 NAG C4 O4 sing N N 269 NAG C4 H4 sing N N 270 NAG C5 C6 sing N N 271 NAG C5 O5 sing N N 272 NAG C5 H5 sing N N 273 NAG C6 O6 sing N N 274 NAG C6 H61 sing N N 275 NAG C6 H62 sing N N 276 NAG C7 C8 sing N N 277 NAG C7 N2 sing N N 278 NAG C7 O7 doub N N 279 NAG C8 H81 sing N N 280 NAG C8 H82 sing N N 281 NAG C8 H83 sing N N 282 NAG N2 HN2 sing N N 283 NAG O1 HO1 sing N N 284 NAG O3 HO3 sing N N 285 NAG O4 HO4 sing N N 286 NAG O6 HO6 sing N N 287 PHE N CA sing N N 288 PHE N H sing N N 289 PHE N H2 sing N N 290 PHE CA C sing N N 291 PHE CA CB sing N N 292 PHE CA HA sing N N 293 PHE C O doub N N 294 PHE C OXT sing N N 295 PHE CB CG sing N N 296 PHE CB HB2 sing N N 297 PHE CB HB3 sing N N 298 PHE CG CD1 doub Y N 299 PHE CG CD2 sing Y N 300 PHE CD1 CE1 sing Y N 301 PHE CD1 HD1 sing N N 302 PHE CD2 CE2 doub Y N 303 PHE CD2 HD2 sing N N 304 PHE CE1 CZ doub Y N 305 PHE CE1 HE1 sing N N 306 PHE CE2 CZ sing Y N 307 PHE CE2 HE2 sing N N 308 PHE CZ HZ sing N N 309 PHE OXT HXT sing N N 310 PRO N CA sing N N 311 PRO N CD sing N N 312 PRO N H sing N N 313 PRO CA C sing N N 314 PRO CA CB sing N N 315 PRO CA HA sing N N 316 PRO C O doub N N 317 PRO C OXT sing N N 318 PRO CB CG sing N N 319 PRO CB HB2 sing N N 320 PRO CB HB3 sing N N 321 PRO CG CD sing N N 322 PRO CG HG2 sing N N 323 PRO CG HG3 sing N N 324 PRO CD HD2 sing N N 325 PRO CD HD3 sing N N 326 PRO OXT HXT sing N N 327 SER N CA sing N N 328 SER N H sing N N 329 SER N H2 sing N N 330 SER CA C sing N N 331 SER CA CB sing N N 332 SER CA HA sing N N 333 SER C O doub N N 334 SER C OXT sing N N 335 SER CB OG sing N N 336 SER CB HB2 sing N N 337 SER CB HB3 sing N N 338 SER OG HG sing N N 339 SER OXT HXT sing N N 340 THR N CA sing N N 341 THR N H sing N N 342 THR N H2 sing N N 343 THR CA C sing N N 344 THR CA CB sing N N 345 THR CA HA sing N N 346 THR C O doub N N 347 THR C OXT sing N N 348 THR CB OG1 sing N N 349 THR CB CG2 sing N N 350 THR CB HB sing N N 351 THR OG1 HG1 sing N N 352 THR CG2 HG21 sing N N 353 THR CG2 HG22 sing N N 354 THR CG2 HG23 sing N N 355 THR OXT HXT sing N N 356 TRP N CA sing N N 357 TRP N H sing N N 358 TRP N H2 sing N N 359 TRP CA C sing N N 360 TRP CA CB sing N N 361 TRP CA HA sing N N 362 TRP C O doub N N 363 TRP C OXT sing N N 364 TRP CB CG sing N N 365 TRP CB HB2 sing N N 366 TRP CB HB3 sing N N 367 TRP CG CD1 doub Y N 368 TRP CG CD2 sing Y N 369 TRP CD1 NE1 sing Y N 370 TRP CD1 HD1 sing N N 371 TRP CD2 CE2 doub Y N 372 TRP CD2 CE3 sing Y N 373 TRP NE1 CE2 sing Y N 374 TRP NE1 HE1 sing N N 375 TRP CE2 CZ2 sing Y N 376 TRP CE3 CZ3 doub Y N 377 TRP CE3 HE3 sing N N 378 TRP CZ2 CH2 doub Y N 379 TRP CZ2 HZ2 sing N N 380 TRP CZ3 CH2 sing Y N 381 TRP CZ3 HZ3 sing N N 382 TRP CH2 HH2 sing N N 383 TRP OXT HXT sing N N 384 TYR N CA sing N N 385 TYR N H sing N N 386 TYR N H2 sing N N 387 TYR CA C sing N N 388 TYR CA CB sing N N 389 TYR CA HA sing N N 390 TYR C O doub N N 391 TYR C OXT sing N N 392 TYR CB CG sing N N 393 TYR CB HB2 sing N N 394 TYR CB HB3 sing N N 395 TYR CG CD1 doub Y N 396 TYR CG CD2 sing Y N 397 TYR CD1 CE1 sing Y N 398 TYR CD1 HD1 sing N N 399 TYR CD2 CE2 doub Y N 400 TYR CD2 HD2 sing N N 401 TYR CE1 CZ doub Y N 402 TYR CE1 HE1 sing N N 403 TYR CE2 CZ sing Y N 404 TYR CE2 HE2 sing N N 405 TYR CZ OH sing N N 406 TYR OH HH sing N N 407 TYR OXT HXT sing N N 408 VAL N CA sing N N 409 VAL N H sing N N 410 VAL N H2 sing N N 411 VAL CA C sing N N 412 VAL CA CB sing N N 413 VAL CA HA sing N N 414 VAL C O doub N N 415 VAL C OXT sing N N 416 VAL CB CG1 sing N N 417 VAL CB CG2 sing N N 418 VAL CB HB sing N N 419 VAL CG1 HG11 sing N N 420 VAL CG1 HG12 sing N N 421 VAL CG1 HG13 sing N N 422 VAL CG2 HG21 sing N N 423 VAL CG2 HG22 sing N N 424 VAL CG2 HG23 sing N N 425 VAL OXT HXT sing N N 426 # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.experimental_flag NO _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.units ? _em_entity_assembly_molwt.value ? # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 9606 _em_entity_assembly_naturalsource.organism 'Homo sapiens' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 1491 _em_entity_assembly_recombinant.organism 'Clostridium botulinum' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 50.8 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 BIOQUANTUM (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged 1 _em_image_recording.num_real_images 6518 # _em_particle_selection.details ? _em_particle_selection.id 1 _em_particle_selection.image_processing_id 1 _em_particle_selection.method ? _em_particle_selection.num_particles_selected 6409122 _em_particle_selection.reference_model ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? cryoSPARC ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? cryoSPARC ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? Coot ? OTHER ? 8 ? ? ? ? ? 'MODEL REFINEMENT' ? 9 ? 1 ? REFMAC ? 'INITIAL EULER ASSIGNMENT' ? 10 1 ? ? cryoSPARC ? 'FINAL EULER ASSIGNMENT' ? 11 1 ? ? cryoSPARC ? CLASSIFICATION ? 12 1 ? ? cryoSPARC ? RECONSTRUCTION ? 13 1 ? ? cryoSPARC ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science (JSPS)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number JP22H02564 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 3 NAG 1 n 3 NAG 2 n 3 FUC 3 n # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 FUC ? ? FUC ? ? 'SUBJECT OF INVESTIGATION' ? 2 NAG ? ? NAG ? ? 'SUBJECT OF INVESTIGATION' ? # _atom_sites.entry_id 8JLE _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # loop_