data_9A32 # _entry.id 9A32 # loop_ _atom_type.symbol C H N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Stahl, K." 1 "Graziadei, A." 2 "Dau, T." 3 "Brock, O." 4 "Rappsilber, J." 5 # loop_ _audit_conform.dict_location _audit_conform.dict_name _audit_conform.dict_version https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_ext.dic mmcif_ihm_ext.dic 1.26 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.395 # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB-Dev PDBDEV_00000187 PDBDEV_00000187 ? PDB 9A32 pdb_00009a32 10.2210/pdb9a32/pdb # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A32 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2023-02-03 # 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 2023-02-24 # _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 ? # _ihm_entry_collection.id PDBDEV_G_1000001 _ihm_entry_collection.name . _ihm_entry_collection.details 'Collection of entries belonging to the publication: "Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning"' # _ihm_entry_collection_mapping.collection_id PDBDEV_G_1000001 _ihm_entry_collection_mapping.entry_id 9A32 # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.094 ALA . ALANINE . "L-peptide linking" "C6 H15 N4 O2 1" 175.212 ARG . ARGININE . "L-peptide linking" "C4 H8 N2 O3" 132.119 ASN . ASPARAGINE . "L-peptide linking" "C4 H7 N O4" 133.103 ASP . "ASPARTIC ACID" . "L-peptide linking" "C5 H10 N2 O3" 146.146 GLN . GLUTAMINE . "L-peptide linking" "C5 H9 N O4" 147.13 GLU . "GLUTAMIC ACID" . "L-peptide linking" "C2 H5 N O2" 75.067 GLY . GLYCINE . "peptide linking" "C6 H10 N3 O2 1" 156.165 HIS . HISTIDINE . "L-peptide linking" "C6 H13 N O2" 131.175 ILE . ISOLEUCINE . "L-peptide linking" "C6 H13 N O2" 131.175 LEU . LEUCINE . "L-peptide linking" "C6 H15 N2 O2 1" 147.198 LYS . LYSINE . "L-peptide linking" "C5 H11 N O2 S" 149.208 MET . METHIONINE . "L-peptide linking" "C9 H11 N O2" 165.192 PHE . PHENYLALANINE . "L-peptide linking" "C5 H9 N O2" 115.132 PRO . PROLINE . "L-peptide linking" "C3 H7 N O3" 105.093 SER . SERINE . "L-peptide linking" "C4 H9 N O3" 119.12 THR . THREONINE . "L-peptide linking" "C11 H12 N2 O2" 204.229 TRP . TRYPTOPHAN . "L-peptide linking" "C9 H11 N O3" 181.191 TYR . TYROSINE . "L-peptide linking" "C5 H11 N O2" 117.148 VAL . VALINE . "L-peptide linking" # _citation.country . _citation.id 1 _citation.journal_abbrev "Nature Biotechnology" _citation.journal_id_ASTM . _citation.journal_id_CSD . _citation.journal_id_ISSN . _citation.journal_issue . _citation.journal_volume . _citation.page_first . _citation.page_last . _citation.pdbx_database_id_DOI 10.1038/s41587-023-01704-z _citation.pdbx_database_id_PubMed 36941363 _citation.title "Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning" _citation.year 2023 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Stahl, K." 1 1 "Graziadei, A." 2 1 "Dau, T." 3 1 "Brock, O." 4 1 "Rappsilber, J." 5 # _entity.details . _entity.formula_weight 46992.93 _entity.id 1 _entity.pdbx_description P06996 _entity.pdbx_number_of_molecules 1 _entity.src_method NAT _entity.type polymer # _entity_poly.entity_id 1 _entity_poly.nstd_chirality . _entity_poly.nstd_linkage NO _entity_poly.nstd_monomer NO _entity_poly.pdbx_seq_one_letter_code MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF _entity_poly.pdbx_seq_one_letter_code_can MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF _entity_poly.pdbx_sequence_evidence_code . _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 . MET 1 1 . LYS 2 1 . VAL 3 1 . LYS 4 1 . VAL 5 1 . LEU 6 1 . SER 7 1 . LEU 8 1 . LEU 9 1 . VAL 10 1 . PRO 11 1 . ALA 12 1 . LEU 13 1 . LEU 14 1 . VAL 15 1 . ALA 16 1 . GLY 17 1 . ALA 18 1 . ALA 19 1 . ASN 20 1 . ALA 21 1 . ALA 22 1 . GLU 23 1 . VAL 24 1 . TYR 25 1 . ASN 26 1 . LYS 27 1 . ASP 28 1 . GLY 29 1 . ASN 30 1 . LYS 31 1 . LEU 32 1 . ASP 33 1 . LEU 34 1 . TYR 35 1 . GLY 36 1 . LYS 37 1 . VAL 38 1 . ASP 39 1 . GLY 40 1 . LEU 41 1 . HIS 42 1 . TYR 43 1 . PHE 44 1 . SER 45 1 . ASP 46 1 . ASN 47 1 . LYS 48 1 . ASP 49 1 . VAL 50 1 . ASP 51 1 . GLY 52 1 . ASP 53 1 . GLN 54 1 . THR 55 1 . TYR 56 1 . MET 57 1 . ARG 58 1 . LEU 59 1 . GLY 60 1 . PHE 61 1 . LYS 62 1 . GLY 63 1 . GLU 64 1 . THR 65 1 . GLN 66 1 . VAL 67 1 . THR 68 1 . ASP 69 1 . GLN 70 1 . LEU 71 1 . THR 72 1 . GLY 73 1 . TYR 74 1 . GLY 75 1 . GLN 76 1 . TRP 77 1 . GLU 78 1 . TYR 79 1 . GLN 80 1 . ILE 81 1 . GLN 82 1 . GLY 83 1 . ASN 84 1 . SER 85 1 . ALA 86 1 . GLU 87 1 . ASN 88 1 . GLU 89 1 . ASN 90 1 . ASN 91 1 . SER 92 1 . TRP 93 1 . THR 94 1 . ARG 95 1 . VAL 96 1 . ALA 97 1 . PHE 98 1 . ALA 99 1 . GLY 100 1 . LEU 101 1 . LYS 102 1 . PHE 103 1 . GLN 104 1 . ASP 105 1 . VAL 106 1 . GLY 107 1 . SER 108 1 . PHE 109 1 . ASP 110 1 . TYR 111 1 . GLY 112 1 . ARG 113 1 . ASN 114 1 . TYR 115 1 . GLY 116 1 . VAL 117 1 . VAL 118 1 . TYR 119 1 . ASP 120 1 . VAL 121 1 . THR 122 1 . SER 123 1 . TRP 124 1 . THR 125 1 . ASP 126 1 . VAL 127 1 . LEU 128 1 . PRO 129 1 . GLU 130 1 . PHE 131 1 . GLY 132 1 . GLY 133 1 . ASP 134 1 . THR 135 1 . TYR 136 1 . GLY 137 1 . SER 138 1 . ASP 139 1 . ASN 140 1 . PHE 141 1 . MET 142 1 . GLN 143 1 . GLN 144 1 . ARG 145 1 . GLY 146 1 . ASN 147 1 . GLY 148 1 . PHE 149 1 . ALA 150 1 . THR 151 1 . TYR 152 1 . ARG 153 1 . ASN 154 1 . THR 155 1 . ASP 156 1 . PHE 157 1 . PHE 158 1 . GLY 159 1 . LEU 160 1 . VAL 161 1 . ASP 162 1 . GLY 163 1 . LEU 164 1 . ASN 165 1 . PHE 166 1 . ALA 167 1 . VAL 168 1 . GLN 169 1 . TYR 170 1 . GLN 171 1 . GLY 172 1 . LYS 173 1 . ASN 174 1 . GLY 175 1 . ASN 176 1 . PRO 177 1 . SER 178 1 . GLY 179 1 . GLU 180 1 . GLY 181 1 . PHE 182 1 . THR 183 1 . SER 184 1 . GLY 185 1 . VAL 186 1 . THR 187 1 . ASN 188 1 . ASN 189 1 . GLY 190 1 . ARG 191 1 . ASP 192 1 . ALA 193 1 . LEU 194 1 . ARG 195 1 . GLN 196 1 . ASN 197 1 . GLY 198 1 . ASP 199 1 . GLY 200 1 . VAL 201 1 . GLY 202 1 . GLY 203 1 . SER 204 1 . ILE 205 1 . THR 206 1 . TYR 207 1 . ASP 208 1 . TYR 209 1 . GLU 210 1 . GLY 211 1 . PHE 212 1 . GLY 213 1 . ILE 214 1 . GLY 215 1 . GLY 216 1 . ALA 217 1 . ILE 218 1 . SER 219 1 . SER 220 1 . SER 221 1 . LYS 222 1 . ARG 223 1 . THR 224 1 . ASP 225 1 . ALA 226 1 . GLN 227 1 . ASN 228 1 . THR 229 1 . ALA 230 1 . ALA 231 1 . TYR 232 1 . ILE 233 1 . GLY 234 1 . ASN 235 1 . GLY 236 1 . ASP 237 1 . ARG 238 1 . ALA 239 1 . GLU 240 1 . THR 241 1 . TYR 242 1 . THR 243 1 . GLY 244 1 . GLY 245 1 . LEU 246 1 . LYS 247 1 . TYR 248 1 . ASP 249 1 . ALA 250 1 . ASN 251 1 . ASN 252 1 . ILE 253 1 . TYR 254 1 . LEU 255 1 . ALA 256 1 . ALA 257 1 . GLN 258 1 . TYR 259 1 . THR 260 1 . GLN 261 1 . THR 262 1 . TYR 263 1 . ASN 264 1 . ALA 265 1 . THR 266 1 . ARG 267 1 . VAL 268 1 . GLY 269 1 . SER 270 1 . LEU 271 1 . GLY 272 1 . TRP 273 1 . ALA 274 1 . ASN 275 1 . LYS 276 1 . ALA 277 1 . GLN 278 1 . ASN 279 1 . PHE 280 1 . GLU 281 1 . ALA 282 1 . VAL 283 1 . ALA 284 1 . GLN 285 1 . TYR 286 1 . GLN 287 1 . PHE 288 1 . ASP 289 1 . PHE 290 1 . GLY 291 1 . LEU 292 1 . ARG 293 1 . PRO 294 1 . SER 295 1 . LEU 296 1 . ALA 297 1 . TYR 298 1 . LEU 299 1 . GLN 300 1 . SER 301 1 . LYS 302 1 . GLY 303 1 . LYS 304 1 . ASN 305 1 . LEU 306 1 . GLY 307 1 . ARG 308 1 . GLY 309 1 . TYR 310 1 . ASP 311 1 . ASP 312 1 . GLU 313 1 . ASP 314 1 . ILE 315 1 . LEU 316 1 . LYS 317 1 . TYR 318 1 . VAL 319 1 . ASP 320 1 . VAL 321 1 . GLY 322 1 . ALA 323 1 . THR 324 1 . TYR 325 1 . TYR 326 1 . PHE 327 1 . ASN 328 1 . LYS 329 1 . ASN 330 1 . MET 331 1 . SER 332 1 . THR 333 1 . TYR 334 1 . VAL 335 1 . ASP 336 1 . TYR 337 1 . LYS 338 1 . ILE 339 1 . ASN 340 1 . LEU 341 1 . LEU 342 1 . ASP 343 1 . ASP 344 1 . ASN 345 1 . GLN 346 1 . PHE 347 1 . THR 348 1 . ARG 349 1 . ASP 350 1 . ALA 351 1 . GLY 352 1 . ILE 353 1 . ASN 354 1 . THR 355 1 . ASP 356 1 . ASN 357 1 . ILE 358 1 . VAL 359 1 . ALA 360 1 . LEU 361 1 . GLY 362 1 . LEU 363 1 . VAL 364 1 . TYR 365 1 . GLN 366 1 . PHE 367 # _ihm_chemical_component_descriptor.auth_name L-Photo-Leucine _ihm_chemical_component_descriptor.chemical_name . _ihm_chemical_component_descriptor.common_name L-Photo-Leucine _ihm_chemical_component_descriptor.details . _ihm_chemical_component_descriptor.id 1 _ihm_chemical_component_descriptor.inchi 1S/C5H9N3O2/c1-5(7-8-5)2-3(6)4(9)10/h3H,2,6H2,1H3,(H,9,10)/t3-/m0/s1 _ihm_chemical_component_descriptor.inchi_key MJRDGTVDJKACQZ-VKHMYHEASA-N _ihm_chemical_component_descriptor.smiles CC1(C[C@H](N)C(O)=O)N=N1 _ihm_chemical_component_descriptor.smiles_canonical . # loop_ _ihm_cross_link_list.comp_id_1 _ihm_cross_link_list.comp_id_2 _ihm_cross_link_list.dataset_list_id _ihm_cross_link_list.details _ihm_cross_link_list.entity_description_1 _ihm_cross_link_list.entity_description_2 _ihm_cross_link_list.entity_id_1 _ihm_cross_link_list.entity_id_2 _ihm_cross_link_list.group_id _ihm_cross_link_list.id _ihm_cross_link_list.linker_chem_comp_descriptor_id _ihm_cross_link_list.linker_type _ihm_cross_link_list.seq_id_1 _ihm_cross_link_list.seq_id_2 ASP LEU 1 . P06996 P06996 1 1 1 1 1 L-Photo-Leucine 314 342 ASP LEU 1 . P06996 P06996 1 1 2 2 1 L-Photo-Leucine 312 342 GLU LEU 1 . P06996 P06996 1 1 3 3 1 L-Photo-Leucine 313 342 ILE LEU 1 . P06996 P06996 1 1 4 4 1 L-Photo-Leucine 315 342 LEU ILE 1 . P06996 P06996 1 1 5 5 1 L-Photo-Leucine 316 339 LEU PHE 1 . P06996 P06996 1 1 6 6 1 L-Photo-Leucine 34 367 LEU LEU 1 . P06996 P06996 1 1 7 7 1 L-Photo-Leucine 316 342 ASP LEU 1 . P06996 P06996 1 1 8 8 1 L-Photo-Leucine 314 341 GLY LEU 1 . P06996 P06996 1 1 9 9 1 L-Photo-Leucine 309 342 ILE LEU 1 . P06996 P06996 1 1 10 10 1 L-Photo-Leucine 315 341 ASP LEU 1 . P06996 P06996 1 1 11 11 1 L-Photo-Leucine 311 342 TYR LEU 1 . P06996 P06996 1 1 12 12 1 L-Photo-Leucine 310 342 GLU LEU 1 . P06996 P06996 1 1 13 13 1 L-Photo-Leucine 313 341 LEU ASP 1 . P06996 P06996 1 1 14 14 1 L-Photo-Leucine 271 356 LEU PHE 1 . P06996 P06996 1 1 15 15 1 L-Photo-Leucine 32 367 LEU LEU 1 . P06996 P06996 1 1 16 16 1 L-Photo-Leucine 316 341 LEU ASN 1 . P06996 P06996 1 1 17 17 1 L-Photo-Leucine 316 340 ASP LEU 1 . P06996 P06996 1 1 18 18 1 L-Photo-Leucine 49 341 LYS LEU 1 . P06996 P06996 1 1 19 19 1 L-Photo-Leucine 317 342 LEU ASP 1 . P06996 P06996 1 1 20 20 1 L-Photo-Leucine 128 320 LEU ASP 1 . P06996 P06996 1 1 21 21 1 L-Photo-Leucine 271 312 ASP LEU 1 . P06996 P06996 1 1 22 22 1 L-Photo-Leucine 49 342 ASN LEU 1 . P06996 P06996 1 1 23 23 1 L-Photo-Leucine 47 341 # loop_ _ihm_cross_link_restraint.asym_id_1 _ihm_cross_link_restraint.asym_id_2 _ihm_cross_link_restraint.atom_id_1 _ihm_cross_link_restraint.atom_id_2 _ihm_cross_link_restraint.comp_id_1 _ihm_cross_link_restraint.comp_id_2 _ihm_cross_link_restraint.conditional_crosslink_flag _ihm_cross_link_restraint.distance_threshold _ihm_cross_link_restraint.entity_id_1 _ihm_cross_link_restraint.entity_id_2 _ihm_cross_link_restraint.group_id _ihm_cross_link_restraint.id _ihm_cross_link_restraint.model_granularity _ihm_cross_link_restraint.pseudo_site_flag _ihm_cross_link_restraint.psi _ihm_cross_link_restraint.restraint_type _ihm_cross_link_restraint.seq_id_1 _ihm_cross_link_restraint.seq_id_2 _ihm_cross_link_restraint.sigma_1 _ihm_cross_link_restraint.sigma_2 A A . . ASP LEU . 10 1 1 1 1 by-residue NO 0.05 "upper bound" 314 342 . . A A . . ASP LEU . 10 1 1 2 2 by-residue NO 0.05 "upper bound" 312 342 . . A A . . GLU LEU . 10 1 1 3 3 by-residue NO 0.05 "upper bound" 313 342 . . A A . . ILE LEU . 10 1 1 4 4 by-residue NO 0.05 "upper bound" 315 342 . . A A . . LEU ILE . 10 1 1 5 5 by-residue NO 0.05 "upper bound" 316 339 . . A A . . LEU PHE . 10 1 1 6 6 by-residue NO 0.05 "upper bound" 34 367 . . A A . . LEU LEU . 10 1 1 7 7 by-residue NO 0.05 "upper bound" 316 342 . . A A . . ASP LEU . 10 1 1 8 8 by-residue NO 0.05 "upper bound" 314 341 . . A A . . GLY LEU . 10 1 1 9 9 by-residue NO 0.05 "upper bound" 309 342 . . A A . . ILE LEU . 10 1 1 10 10 by-residue NO 0.05 "upper bound" 315 341 . . A A . . ASP LEU . 10 1 1 11 11 by-residue NO 0.05 "upper bound" 311 342 . . A A . . TYR LEU . 10 1 1 12 12 by-residue NO 0.05 "upper bound" 310 342 . . A A . . GLU LEU . 10 1 1 13 13 by-residue NO 0.05 "upper bound" 313 341 . . A A . . LEU ASP . 10 1 1 14 14 by-residue NO 0.05 "upper bound" 271 356 . . A A . . LEU PHE . 10 1 1 15 15 by-residue NO 0.05 "upper bound" 32 367 . . A A . . LEU LEU . 10 1 1 16 16 by-residue NO 0.05 "upper bound" 316 341 . . A A . . LEU ASN . 10 1 1 17 17 by-residue NO 0.05 "upper bound" 316 340 . . A A . . ASP LEU . 10 1 1 18 18 by-residue NO 0.05 "upper bound" 49 341 . . A A . . LYS LEU . 10 1 1 19 19 by-residue NO 0.05 "upper bound" 317 342 . . A A . . LEU ASP . 10 1 1 20 20 by-residue NO 0.05 "upper bound" 128 320 . . A A . . LEU ASP . 10 1 1 21 21 by-residue NO 0.05 "upper bound" 271 312 . . A A . . ASP LEU . 10 1 1 22 22 by-residue NO 0.05 "upper bound" 49 342 . . A A . . ASN LEU . 10 1 1 23 23 by-residue NO 0.05 "upper bound" 47 341 . . # _ihm_dataset_group.application . _ihm_dataset_group.details . _ihm_dataset_group.id 1 _ihm_dataset_group.name . # _ihm_dataset_group_link.dataset_list_id 1 _ihm_dataset_group_link.group_id 1 # _ihm_dataset_list.data_type "Crosslinking-MS data" _ihm_dataset_list.database_hosted YES _ihm_dataset_list.details . _ihm_dataset_list.id 1 # _ihm_dataset_related_db_reference.accession_code JPST001851 _ihm_dataset_related_db_reference.dataset_list_id 1 _ihm_dataset_related_db_reference.db_name jPOSTrepo _ihm_dataset_related_db_reference.details . _ihm_dataset_related_db_reference.id 1 _ihm_dataset_related_db_reference.version . # _ihm_entity_poly_segment.comp_id_begin MET _ihm_entity_poly_segment.comp_id_end PHE _ihm_entity_poly_segment.entity_id 1 _ihm_entity_poly_segment.id 1 _ihm_entity_poly_segment.seq_id_begin 1 _ihm_entity_poly_segment.seq_id_end 367 # _ihm_model_group.details . _ihm_model_group.id 1 _ihm_model_group.name . # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 # loop_ _ihm_model_list.assembly_id _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 1 . 1 1 1 2 . 1 1 1 3 . 1 1 1 4 . 1 1 1 5 . 1 1 1 6 . 1 1 1 7 . 1 1 1 8 . 1 1 1 9 . 1 1 1 10 . 1 1 # _ihm_model_representation.details . _ihm_model_representation.id 1 _ihm_model_representation.name . # _ihm_model_representation_details.description . _ihm_model_representation_details.entity_asym_id A _ihm_model_representation_details.entity_description P06996 _ihm_model_representation_details.entity_id 1 _ihm_model_representation_details.entity_poly_segment_id 1 _ihm_model_representation_details.id 1 _ihm_model_representation_details.model_granularity by-atom _ihm_model_representation_details.model_mode flexible _ihm_model_representation_details.model_object_count . _ihm_model_representation_details.model_object_primitive atomistic _ihm_model_representation_details.representation_id 1 _ihm_model_representation_details.starting_model_id . # _ihm_modeling_protocol.details . _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 1 _ihm_modeling_protocol.protocol_name AlphaLink # _ihm_modeling_protocol_details.dataset_group_id 1 _ihm_modeling_protocol_details.description . _ihm_modeling_protocol_details.ensemble_flag YES _ihm_modeling_protocol_details.id 1 _ihm_modeling_protocol_details.multi_scale_flag NO _ihm_modeling_protocol_details.multi_state_flag NO _ihm_modeling_protocol_details.num_models_begin 0 _ihm_modeling_protocol_details.num_models_end 10 _ihm_modeling_protocol_details.ordered_flag NO _ihm_modeling_protocol_details.protocol_id 1 _ihm_modeling_protocol_details.script_file_id . _ihm_modeling_protocol_details.software_id . _ihm_modeling_protocol_details.step_id 1 _ihm_modeling_protocol_details.step_method "AlphaLink with 10 msa subsamples" _ihm_modeling_protocol_details.step_name AlphaLink _ihm_modeling_protocol_details.struct_assembly_description . _ihm_modeling_protocol_details.struct_assembly_id 1 # _ihm_struct_assembly.description "Integrative modeling using in-cell photo-crosslinking mass spectrometry and deep learning" _ihm_struct_assembly.id 1 _ihm_struct_assembly.name "Integrative model" # _ihm_struct_assembly_details.assembly_id 1 _ihm_struct_assembly_details.asym_id A _ihm_struct_assembly_details.entity_description P06996 _ihm_struct_assembly_details.entity_id 1 _ihm_struct_assembly_details.entity_poly_segment_id 1 _ihm_struct_assembly_details.id 1 _ihm_struct_assembly_details.parent_assembly_id 1 # _software.citation_id 1 _software.classification "model building" _software.description "protein structure prediction by deep learning assisted by experimental distance restraints" _software.location https://github.com/lhatsk/AlphaLink _software.name AlphaLink _software.pdbx_ordinal 1 _software.type program _software.version 1.0 # _struct.entry_id 9A32 _struct.pdbx_CASP_flag . _struct.pdbx_descriptor . _struct.pdbx_details . _struct.pdbx_model_details . _struct.pdbx_model_type_details . _struct.title "Model of E. coli OmpC by in-cell photo-crosslinking MS and deep learning" _struct.pdbx_structure_determination_methodology integrative # _struct_asym.details P06996 _struct_asym.entity_id 1 _struct_asym.id A _struct_asym.pdbx_PDB_id . _struct_asym.pdbx_alt_id . _struct_asym.pdbx_blank_PDB_chainid_flag . _struct_asym.pdbx_modified . _struct_asym.pdbx_order . _struct_asym.pdbx_type . # _struct_ref.db_code OMPC_ECOLI _struct_ref.db_name UNP _struct_ref.details "Outer membrane porin C OS=Escherichia coli (strain K12) OX=83333 GN=ompC PE=1 SV=1" _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession P06996 _struct_ref.pdbx_seq_one_letter_code MKVKVLSLLVPALLVAGAANAAEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.db_align_end 367 _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 367 # 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.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 A 1 1 MET 1 1 MET MET A . A 1 2 LYS 2 2 LYS LYS A . A 1 3 VAL 3 3 VAL VAL A . A 1 4 LYS 4 4 LYS LYS A . A 1 5 VAL 5 5 VAL VAL A . A 1 6 LEU 6 6 LEU LEU A . A 1 7 SER 7 7 SER SER A . A 1 8 LEU 8 8 LEU LEU A . A 1 9 LEU 9 9 LEU LEU A . A 1 10 VAL 10 10 VAL VAL A . A 1 11 PRO 11 11 PRO PRO A . A 1 12 ALA 12 12 ALA ALA A . A 1 13 LEU 13 13 LEU LEU A . A 1 14 LEU 14 14 LEU LEU A . A 1 15 VAL 15 15 VAL VAL A . A 1 16 ALA 16 16 ALA ALA A . A 1 17 GLY 17 17 GLY GLY A . A 1 18 ALA 18 18 ALA ALA A . A 1 19 ALA 19 19 ALA ALA A . A 1 20 ASN 20 20 ASN ASN A . A 1 21 ALA 21 21 ALA ALA A . A 1 22 ALA 22 22 ALA ALA A . A 1 23 GLU 23 23 GLU GLU A . A 1 24 VAL 24 24 VAL VAL A . A 1 25 TYR 25 25 TYR TYR A . A 1 26 ASN 26 26 ASN ASN A . A 1 27 LYS 27 27 LYS LYS A . A 1 28 ASP 28 28 ASP ASP A . A 1 29 GLY 29 29 GLY GLY A . A 1 30 ASN 30 30 ASN ASN A . A 1 31 LYS 31 31 LYS LYS A . A 1 32 LEU 32 32 LEU LEU A . A 1 33 ASP 33 33 ASP ASP A . A 1 34 LEU 34 34 LEU LEU A . A 1 35 TYR 35 35 TYR TYR A . A 1 36 GLY 36 36 GLY GLY A . A 1 37 LYS 37 37 LYS LYS A . A 1 38 VAL 38 38 VAL VAL A . A 1 39 ASP 39 39 ASP ASP A . A 1 40 GLY 40 40 GLY GLY A . A 1 41 LEU 41 41 LEU LEU A . A 1 42 HIS 42 42 HIS HIS A . A 1 43 TYR 43 43 TYR TYR A . A 1 44 PHE 44 44 PHE PHE A . A 1 45 SER 45 45 SER SER A . A 1 46 ASP 46 46 ASP ASP A . A 1 47 ASN 47 47 ASN ASN A . A 1 48 LYS 48 48 LYS LYS A . A 1 49 ASP 49 49 ASP ASP A . A 1 50 VAL 50 50 VAL VAL A . A 1 51 ASP 51 51 ASP ASP A . A 1 52 GLY 52 52 GLY GLY A . A 1 53 ASP 53 53 ASP ASP A . A 1 54 GLN 54 54 GLN GLN A . A 1 55 THR 55 55 THR THR A . A 1 56 TYR 56 56 TYR TYR A . A 1 57 MET 57 57 MET MET A . A 1 58 ARG 58 58 ARG ARG A . A 1 59 LEU 59 59 LEU LEU A . A 1 60 GLY 60 60 GLY GLY A . A 1 61 PHE 61 61 PHE PHE A . A 1 62 LYS 62 62 LYS LYS A . A 1 63 GLY 63 63 GLY GLY A . A 1 64 GLU 64 64 GLU GLU A . A 1 65 THR 65 65 THR THR A . A 1 66 GLN 66 66 GLN GLN A . A 1 67 VAL 67 67 VAL VAL A . A 1 68 THR 68 68 THR THR A . A 1 69 ASP 69 69 ASP ASP A . A 1 70 GLN 70 70 GLN GLN A . A 1 71 LEU 71 71 LEU LEU A . A 1 72 THR 72 72 THR THR A . A 1 73 GLY 73 73 GLY GLY A . A 1 74 TYR 74 74 TYR TYR A . A 1 75 GLY 75 75 GLY GLY A . A 1 76 GLN 76 76 GLN GLN A . A 1 77 TRP 77 77 TRP TRP A . A 1 78 GLU 78 78 GLU GLU A . A 1 79 TYR 79 79 TYR TYR A . A 1 80 GLN 80 80 GLN GLN A . A 1 81 ILE 81 81 ILE ILE A . A 1 82 GLN 82 82 GLN GLN A . A 1 83 GLY 83 83 GLY GLY A . A 1 84 ASN 84 84 ASN ASN A . A 1 85 SER 85 85 SER SER A . A 1 86 ALA 86 86 ALA ALA A . A 1 87 GLU 87 87 GLU GLU A . A 1 88 ASN 88 88 ASN ASN A . A 1 89 GLU 89 89 GLU GLU A . A 1 90 ASN 90 90 ASN ASN A . A 1 91 ASN 91 91 ASN ASN A . A 1 92 SER 92 92 SER SER A . A 1 93 TRP 93 93 TRP TRP A . A 1 94 THR 94 94 THR THR A . A 1 95 ARG 95 95 ARG ARG A . A 1 96 VAL 96 96 VAL VAL A . A 1 97 ALA 97 97 ALA ALA A . A 1 98 PHE 98 98 PHE PHE A . A 1 99 ALA 99 99 ALA ALA A . A 1 100 GLY 100 100 GLY GLY A . A 1 101 LEU 101 101 LEU LEU A . A 1 102 LYS 102 102 LYS LYS A . A 1 103 PHE 103 103 PHE PHE A . A 1 104 GLN 104 104 GLN GLN A . A 1 105 ASP 105 105 ASP ASP A . A 1 106 VAL 106 106 VAL VAL A . A 1 107 GLY 107 107 GLY GLY A . A 1 108 SER 108 108 SER SER A . A 1 109 PHE 109 109 PHE PHE A . A 1 110 ASP 110 110 ASP ASP A . A 1 111 TYR 111 111 TYR TYR A . A 1 112 GLY 112 112 GLY GLY A . A 1 113 ARG 113 113 ARG ARG A . A 1 114 ASN 114 114 ASN ASN A . A 1 115 TYR 115 115 TYR TYR A . A 1 116 GLY 116 116 GLY GLY A . A 1 117 VAL 117 117 VAL VAL A . A 1 118 VAL 118 118 VAL VAL A . A 1 119 TYR 119 119 TYR TYR A . A 1 120 ASP 120 120 ASP ASP A . A 1 121 VAL 121 121 VAL VAL A . A 1 122 THR 122 122 THR THR A . A 1 123 SER 123 123 SER SER A . A 1 124 TRP 124 124 TRP TRP A . A 1 125 THR 125 125 THR THR A . A 1 126 ASP 126 126 ASP ASP A . A 1 127 VAL 127 127 VAL VAL A . A 1 128 LEU 128 128 LEU LEU A . A 1 129 PRO 129 129 PRO PRO A . A 1 130 GLU 130 130 GLU GLU A . A 1 131 PHE 131 131 PHE PHE A . A 1 132 GLY 132 132 GLY GLY A . A 1 133 GLY 133 133 GLY GLY A . A 1 134 ASP 134 134 ASP ASP A . A 1 135 THR 135 135 THR THR A . A 1 136 TYR 136 136 TYR TYR A . A 1 137 GLY 137 137 GLY GLY A . A 1 138 SER 138 138 SER SER A . A 1 139 ASP 139 139 ASP ASP A . A 1 140 ASN 140 140 ASN ASN A . A 1 141 PHE 141 141 PHE PHE A . A 1 142 MET 142 142 MET MET A . A 1 143 GLN 143 143 GLN GLN A . A 1 144 GLN 144 144 GLN GLN A . A 1 145 ARG 145 145 ARG ARG A . A 1 146 GLY 146 146 GLY GLY A . A 1 147 ASN 147 147 ASN ASN A . A 1 148 GLY 148 148 GLY GLY A . A 1 149 PHE 149 149 PHE PHE A . A 1 150 ALA 150 150 ALA ALA A . A 1 151 THR 151 151 THR THR A . A 1 152 TYR 152 152 TYR TYR A . A 1 153 ARG 153 153 ARG ARG A . A 1 154 ASN 154 154 ASN ASN A . A 1 155 THR 155 155 THR THR A . A 1 156 ASP 156 156 ASP ASP A . A 1 157 PHE 157 157 PHE PHE A . A 1 158 PHE 158 158 PHE PHE A . A 1 159 GLY 159 159 GLY GLY A . A 1 160 LEU 160 160 LEU LEU A . A 1 161 VAL 161 161 VAL VAL A . A 1 162 ASP 162 162 ASP ASP A . A 1 163 GLY 163 163 GLY GLY A . A 1 164 LEU 164 164 LEU LEU A . A 1 165 ASN 165 165 ASN ASN A . A 1 166 PHE 166 166 PHE PHE A . A 1 167 ALA 167 167 ALA ALA A . A 1 168 VAL 168 168 VAL VAL A . A 1 169 GLN 169 169 GLN GLN A . A 1 170 TYR 170 170 TYR TYR A . A 1 171 GLN 171 171 GLN GLN A . A 1 172 GLY 172 172 GLY GLY A . A 1 173 LYS 173 173 LYS LYS A . A 1 174 ASN 174 174 ASN ASN A . A 1 175 GLY 175 175 GLY GLY A . A 1 176 ASN 176 176 ASN ASN A . A 1 177 PRO 177 177 PRO PRO A . A 1 178 SER 178 178 SER SER A . A 1 179 GLY 179 179 GLY GLY A . A 1 180 GLU 180 180 GLU GLU A . A 1 181 GLY 181 181 GLY GLY A . A 1 182 PHE 182 182 PHE PHE A . A 1 183 THR 183 183 THR THR A . A 1 184 SER 184 184 SER SER A . A 1 185 GLY 185 185 GLY GLY A . A 1 186 VAL 186 186 VAL VAL A . A 1 187 THR 187 187 THR THR A . A 1 188 ASN 188 188 ASN ASN A . A 1 189 ASN 189 189 ASN ASN A . A 1 190 GLY 190 190 GLY GLY A . A 1 191 ARG 191 191 ARG ARG A . A 1 192 ASP 192 192 ASP ASP A . A 1 193 ALA 193 193 ALA ALA A . A 1 194 LEU 194 194 LEU LEU A . A 1 195 ARG 195 195 ARG ARG A . A 1 196 GLN 196 196 GLN GLN A . A 1 197 ASN 197 197 ASN ASN A . A 1 198 GLY 198 198 GLY GLY A . A 1 199 ASP 199 199 ASP ASP A . A 1 200 GLY 200 200 GLY GLY A . A 1 201 VAL 201 201 VAL VAL A . A 1 202 GLY 202 202 GLY GLY A . A 1 203 GLY 203 203 GLY GLY A . A 1 204 SER 204 204 SER SER A . A 1 205 ILE 205 205 ILE ILE A . A 1 206 THR 206 206 THR THR A . A 1 207 TYR 207 207 TYR TYR A . A 1 208 ASP 208 208 ASP ASP A . A 1 209 TYR 209 209 TYR TYR A . A 1 210 GLU 210 210 GLU GLU A . A 1 211 GLY 211 211 GLY GLY A . A 1 212 PHE 212 212 PHE PHE A . A 1 213 GLY 213 213 GLY GLY A . A 1 214 ILE 214 214 ILE ILE A . A 1 215 GLY 215 215 GLY GLY A . A 1 216 GLY 216 216 GLY GLY A . A 1 217 ALA 217 217 ALA ALA A . A 1 218 ILE 218 218 ILE ILE A . A 1 219 SER 219 219 SER SER A . A 1 220 SER 220 220 SER SER A . A 1 221 SER 221 221 SER SER A . A 1 222 LYS 222 222 LYS LYS A . A 1 223 ARG 223 223 ARG ARG A . A 1 224 THR 224 224 THR THR A . A 1 225 ASP 225 225 ASP ASP A . A 1 226 ALA 226 226 ALA ALA A . A 1 227 GLN 227 227 GLN GLN A . A 1 228 ASN 228 228 ASN ASN A . A 1 229 THR 229 229 THR THR A . A 1 230 ALA 230 230 ALA ALA A . A 1 231 ALA 231 231 ALA ALA A . A 1 232 TYR 232 232 TYR TYR A . A 1 233 ILE 233 233 ILE ILE A . A 1 234 GLY 234 234 GLY GLY A . A 1 235 ASN 235 235 ASN ASN A . A 1 236 GLY 236 236 GLY GLY A . A 1 237 ASP 237 237 ASP ASP A . A 1 238 ARG 238 238 ARG ARG A . A 1 239 ALA 239 239 ALA ALA A . A 1 240 GLU 240 240 GLU GLU A . A 1 241 THR 241 241 THR THR A . A 1 242 TYR 242 242 TYR TYR A . A 1 243 THR 243 243 THR THR A . A 1 244 GLY 244 244 GLY GLY A . A 1 245 GLY 245 245 GLY GLY A . A 1 246 LEU 246 246 LEU LEU A . A 1 247 LYS 247 247 LYS LYS A . A 1 248 TYR 248 248 TYR TYR A . A 1 249 ASP 249 249 ASP ASP A . A 1 250 ALA 250 250 ALA ALA A . A 1 251 ASN 251 251 ASN ASN A . A 1 252 ASN 252 252 ASN ASN A . A 1 253 ILE 253 253 ILE ILE A . A 1 254 TYR 254 254 TYR TYR A . A 1 255 LEU 255 255 LEU LEU A . A 1 256 ALA 256 256 ALA ALA A . A 1 257 ALA 257 257 ALA ALA A . A 1 258 GLN 258 258 GLN GLN A . A 1 259 TYR 259 259 TYR TYR A . A 1 260 THR 260 260 THR THR A . A 1 261 GLN 261 261 GLN GLN A . A 1 262 THR 262 262 THR THR A . A 1 263 TYR 263 263 TYR TYR A . A 1 264 ASN 264 264 ASN ASN A . A 1 265 ALA 265 265 ALA ALA A . A 1 266 THR 266 266 THR THR A . A 1 267 ARG 267 267 ARG ARG A . A 1 268 VAL 268 268 VAL VAL A . A 1 269 GLY 269 269 GLY GLY A . A 1 270 SER 270 270 SER SER A . A 1 271 LEU 271 271 LEU LEU A . A 1 272 GLY 272 272 GLY GLY A . A 1 273 TRP 273 273 TRP TRP A . A 1 274 ALA 274 274 ALA ALA A . A 1 275 ASN 275 275 ASN ASN A . A 1 276 LYS 276 276 LYS LYS A . A 1 277 ALA 277 277 ALA ALA A . A 1 278 GLN 278 278 GLN GLN A . A 1 279 ASN 279 279 ASN ASN A . A 1 280 PHE 280 280 PHE PHE A . A 1 281 GLU 281 281 GLU GLU A . A 1 282 ALA 282 282 ALA ALA A . A 1 283 VAL 283 283 VAL VAL A . A 1 284 ALA 284 284 ALA ALA A . A 1 285 GLN 285 285 GLN GLN A . A 1 286 TYR 286 286 TYR TYR A . A 1 287 GLN 287 287 GLN GLN A . A 1 288 PHE 288 288 PHE PHE A . A 1 289 ASP 289 289 ASP ASP A . A 1 290 PHE 290 290 PHE PHE A . A 1 291 GLY 291 291 GLY GLY A . A 1 292 LEU 292 292 LEU LEU A . A 1 293 ARG 293 293 ARG ARG A . A 1 294 PRO 294 294 PRO PRO A . A 1 295 SER 295 295 SER SER A . A 1 296 LEU 296 296 LEU LEU A . A 1 297 ALA 297 297 ALA ALA A . A 1 298 TYR 298 298 TYR TYR A . A 1 299 LEU 299 299 LEU LEU A . A 1 300 GLN 300 300 GLN GLN A . A 1 301 SER 301 301 SER SER A . A 1 302 LYS 302 302 LYS LYS A . A 1 303 GLY 303 303 GLY GLY A . A 1 304 LYS 304 304 LYS LYS A . A 1 305 ASN 305 305 ASN ASN A . A 1 306 LEU 306 306 LEU LEU A . A 1 307 GLY 307 307 GLY GLY A . A 1 308 ARG 308 308 ARG ARG A . A 1 309 GLY 309 309 GLY GLY A . A 1 310 TYR 310 310 TYR TYR A . A 1 311 ASP 311 311 ASP ASP A . A 1 312 ASP 312 312 ASP ASP A . A 1 313 GLU 313 313 GLU GLU A . A 1 314 ASP 314 314 ASP ASP A . A 1 315 ILE 315 315 ILE ILE A . A 1 316 LEU 316 316 LEU LEU A . A 1 317 LYS 317 317 LYS LYS A . A 1 318 TYR 318 318 TYR TYR A . A 1 319 VAL 319 319 VAL VAL A . A 1 320 ASP 320 320 ASP ASP A . A 1 321 VAL 321 321 VAL VAL A . A 1 322 GLY 322 322 GLY GLY A . A 1 323 ALA 323 323 ALA ALA A . A 1 324 THR 324 324 THR THR A . A 1 325 TYR 325 325 TYR TYR A . A 1 326 TYR 326 326 TYR TYR A . A 1 327 PHE 327 327 PHE PHE A . A 1 328 ASN 328 328 ASN ASN A . A 1 329 LYS 329 329 LYS LYS A . A 1 330 ASN 330 330 ASN ASN A . A 1 331 MET 331 331 MET MET A . A 1 332 SER 332 332 SER SER A . A 1 333 THR 333 333 THR THR A . A 1 334 TYR 334 334 TYR TYR A . A 1 335 VAL 335 335 VAL VAL A . A 1 336 ASP 336 336 ASP ASP A . A 1 337 TYR 337 337 TYR TYR A . A 1 338 LYS 338 338 LYS LYS A . A 1 339 ILE 339 339 ILE ILE A . A 1 340 ASN 340 340 ASN ASN A . A 1 341 LEU 341 341 LEU LEU A . A 1 342 LEU 342 342 LEU LEU A . A 1 343 ASP 343 343 ASP ASP A . A 1 344 ASP 344 344 ASP ASP A . A 1 345 ASN 345 345 ASN ASN A . A 1 346 GLN 346 346 GLN GLN A . A 1 347 PHE 347 347 PHE PHE A . A 1 348 THR 348 348 THR THR A . A 1 349 ARG 349 349 ARG ARG A . A 1 350 ASP 350 350 ASP ASP A . A 1 351 ALA 351 351 ALA ALA A . A 1 352 GLY 352 352 GLY GLY A . A 1 353 ILE 353 353 ILE ILE A . A 1 354 ASN 354 354 ASN ASN A . A 1 355 THR 355 355 THR THR A . A 1 356 ASP 356 356 ASP ASP A . A 1 357 ASN 357 357 ASN ASN A . A 1 358 ILE 358 358 ILE ILE A . A 1 359 VAL 359 359 VAL VAL A . A 1 360 ALA 360 360 ALA ALA A . A 1 361 LEU 361 361 LEU LEU A . A 1 362 GLY 362 362 GLY GLY A . A 1 363 LEU 363 363 LEU LEU A . A 1 364 VAL 364 364 VAL VAL A . A 1 365 TYR 365 365 TYR TYR A . A 1 366 GLN 366 366 GLN GLN A . A 1 367 PHE 367 367 PHE PHE A . # # loop_ # #