data_2YD9 # _entry.id 2YD9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.399 _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 2YD9 pdb_00002yd9 10.2210/pdb2yd9/pdb PDBE EBI-47750 ? ? WWPDB D_1290047750 ? ? # 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 2011-04-13 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2020-07-29 5 'Structure model' 1 4 2023-12-20 6 'Structure model' 1 5 2024-11-20 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 4 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other 6 4 'Structure model' 'Structure summary' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' 9 5 'Structure model' 'Refinement description' 10 5 'Structure model' 'Structure summary' 11 6 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp 2 4 'Structure model' entity 3 4 'Structure model' pdbx_chem_comp_identifier 4 4 'Structure model' pdbx_database_status 5 4 'Structure model' pdbx_entity_nonpoly 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site 8 4 'Structure model' struct_site_gen 9 5 'Structure model' chem_comp 10 5 'Structure model' chem_comp_atom 11 5 'Structure model' chem_comp_bond 12 5 'Structure model' database_2 13 5 'Structure model' pdbx_initial_refinement_model 14 6 'Structure model' pdbx_entry_details 15 6 'Structure model' pdbx_modification_feature # 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 4 'Structure model' '_chem_comp.name' 2 4 'Structure model' '_chem_comp.type' 3 4 'Structure model' '_entity.pdbx_description' 4 4 'Structure model' '_pdbx_database_status.status_code_sf' 5 4 'Structure model' '_pdbx_entity_nonpoly.name' 6 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 4 'Structure model' '_struct_conn.pdbx_role' 8 5 'Structure model' '_chem_comp.pdbx_synonyms' 9 5 'Structure model' '_database_2.pdbx_DOI' 10 5 'Structure model' '_database_2.pdbx_database_accession' 11 6 'Structure model' '_pdbx_entry_details.has_protein_modification' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2YD9 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2011-03-18 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2FH7 unspecified 'CRYSTAL STRUCTURE OF THE PHOSPHATASE DOMAINS OF HUMAN PTPSIGMA' PDB 2YD1 unspecified 'CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF DROSOPHILA RECEPTOR PROTEIN TYROSINE PHOSPHATASE DLAR' PDB 2YD2 unspecified 'CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA' PDB 2YD3 unspecified 'CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA' PDB 2YD4 unspecified 'CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF CHICKEN RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA' PDB 2YD5 unspecified 'CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE LAR' PDB 2YD6 unspecified 'CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE DELTA' PDB 2YD7 unspecified 'CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE DELTA' PDB 2YD8 unspecified ;CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR PROTEIN TYROSINE PHOSPHATASE LAR IN COMPLEX WITH SUCROSE OCTASULPHATE ; # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Coles, C.H.' 1 'Shen, Y.' 2 'Tenney, A.P.' 3 'Siebold, C.' 4 'Sutton, G.C.' 5 'Lu, W.' 6 'Gallagher, J.T.' 7 'Jones, E.Y.' 8 'Flanagan, J.G.' 9 'Aricescu, A.R.' 10 # _citation.id primary _citation.title 'Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension.' _citation.journal_abbrev Science _citation.journal_volume 332 _citation.page_first 484 _citation.page_last ? _citation.year 2011 _citation.journal_id_ASTM SCIEAS _citation.country US _citation.journal_id_ISSN 0036-8075 _citation.journal_id_CSD 0038 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21454754 _citation.pdbx_database_id_DOI 10.1126/SCIENCE.1200840 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Coles, C.H.' 1 ? primary 'Shen, Y.' 2 ? primary 'Tenney, A.P.' 3 ? primary 'Siebold, C.' 4 ? primary 'Sutton, G.C.' 5 ? primary 'Lu, W.' 6 ? primary 'Gallagher, J.T.' 7 ? primary 'Jones, E.Y.' 8 ? primary 'Flanagan, J.G.' 9 ? primary 'Aricescu, A.R.' 10 ? # 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 'RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S' 33261.570 1 3.1.3.48 YES 'IG1-3, RESIDUES 30-321' ? 2 non-polymer syn 'CHLORIDE ION' 35.453 4 ? ? ? ? 3 non-polymer syn 'IODIDE ION' 126.904 4 ? ? ? ? 4 non-polymer man 2-acetamido-2-deoxy-beta-D-glucopyranose 221.208 2 ? ? ? ? 5 non-polymer syn '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' 282.334 1 ? ? ? ? 6 water nat water 18.015 20 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'R-PTP-S, RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA R-PTP-SIGMA, RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;ETGEEPPRFIKEPKDQIGVSGGVASFVCQATGDPKPRVTWNKKGKKVNSQRFETIEFDESAGAVLRIQPLRTPRDENVYE CVAQNSVGEITVHAKLTVLREDQLPSGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSASNGRIKQ LRSGALQIESSEETDQGKYECVATNSAGVRYSSPANLYVRVQNVAPRFSILPMSHEIMPGGNVNITCVAVGSPMPYVKWM QGAEDLTPEDDMPVGRNVLELTDVKDSANYTCVAMSSLGVIEAVAQITVKSLPKAGTKHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;ETGEEPPRFIKEPKDQIGVSGGVASFVCQATGDPKPRVTWNKKGKKVNSQRFETIEFDESAGAVLRIQPLRTPRDENVYE CVAQNSVGEITVHAKLTVLREDQLPSGFPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPSASNGRIKQ LRSGALQIESSEETDQGKYECVATNSAGVRYSSPANLYVRVQNVAPRFSILPMSHEIMPGGNVNITCVAVGSPMPYVKWM QGAEDLTPEDDMPVGRNVLELTDVKDSANYTCVAMSSLGVIEAVAQITVKSLPKAGTKHHHHHH ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CHLORIDE ION' CL 3 'IODIDE ION' IOD 4 2-acetamido-2-deoxy-beta-D-glucopyranose NAG 5 '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' B3P 6 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLU n 1 2 THR n 1 3 GLY n 1 4 GLU n 1 5 GLU n 1 6 PRO n 1 7 PRO n 1 8 ARG n 1 9 PHE n 1 10 ILE n 1 11 LYS n 1 12 GLU n 1 13 PRO n 1 14 LYS n 1 15 ASP n 1 16 GLN n 1 17 ILE n 1 18 GLY n 1 19 VAL n 1 20 SER n 1 21 GLY n 1 22 GLY n 1 23 VAL n 1 24 ALA n 1 25 SER n 1 26 PHE n 1 27 VAL n 1 28 CYS n 1 29 GLN n 1 30 ALA n 1 31 THR n 1 32 GLY n 1 33 ASP n 1 34 PRO n 1 35 LYS n 1 36 PRO n 1 37 ARG n 1 38 VAL n 1 39 THR n 1 40 TRP n 1 41 ASN n 1 42 LYS n 1 43 LYS n 1 44 GLY n 1 45 LYS n 1 46 LYS n 1 47 VAL n 1 48 ASN n 1 49 SER n 1 50 GLN n 1 51 ARG n 1 52 PHE n 1 53 GLU n 1 54 THR n 1 55 ILE n 1 56 GLU n 1 57 PHE n 1 58 ASP n 1 59 GLU n 1 60 SER n 1 61 ALA n 1 62 GLY n 1 63 ALA n 1 64 VAL n 1 65 LEU n 1 66 ARG n 1 67 ILE n 1 68 GLN n 1 69 PRO n 1 70 LEU n 1 71 ARG n 1 72 THR n 1 73 PRO n 1 74 ARG n 1 75 ASP n 1 76 GLU n 1 77 ASN n 1 78 VAL n 1 79 TYR n 1 80 GLU n 1 81 CYS n 1 82 VAL n 1 83 ALA n 1 84 GLN n 1 85 ASN n 1 86 SER n 1 87 VAL n 1 88 GLY n 1 89 GLU n 1 90 ILE n 1 91 THR n 1 92 VAL n 1 93 HIS n 1 94 ALA n 1 95 LYS n 1 96 LEU n 1 97 THR n 1 98 VAL n 1 99 LEU n 1 100 ARG n 1 101 GLU n 1 102 ASP n 1 103 GLN n 1 104 LEU n 1 105 PRO n 1 106 SER n 1 107 GLY n 1 108 PHE n 1 109 PRO n 1 110 ASN n 1 111 ILE n 1 112 ASP n 1 113 MET n 1 114 GLY n 1 115 PRO n 1 116 GLN n 1 117 LEU n 1 118 LYS n 1 119 VAL n 1 120 VAL n 1 121 GLU n 1 122 ARG n 1 123 THR n 1 124 ARG n 1 125 THR n 1 126 ALA n 1 127 THR n 1 128 MET n 1 129 LEU n 1 130 CYS n 1 131 ALA n 1 132 ALA n 1 133 SER n 1 134 GLY n 1 135 ASN n 1 136 PRO n 1 137 ASP n 1 138 PRO n 1 139 GLU n 1 140 ILE n 1 141 THR n 1 142 TRP n 1 143 PHE n 1 144 LYS n 1 145 ASP n 1 146 PHE n 1 147 LEU n 1 148 PRO n 1 149 VAL n 1 150 ASP n 1 151 PRO n 1 152 SER n 1 153 ALA n 1 154 SER n 1 155 ASN n 1 156 GLY n 1 157 ARG n 1 158 ILE n 1 159 LYS n 1 160 GLN n 1 161 LEU n 1 162 ARG n 1 163 SER n 1 164 GLY n 1 165 ALA n 1 166 LEU n 1 167 GLN n 1 168 ILE n 1 169 GLU n 1 170 SER n 1 171 SER n 1 172 GLU n 1 173 GLU n 1 174 THR n 1 175 ASP n 1 176 GLN n 1 177 GLY n 1 178 LYS n 1 179 TYR n 1 180 GLU n 1 181 CYS n 1 182 VAL n 1 183 ALA n 1 184 THR n 1 185 ASN n 1 186 SER n 1 187 ALA n 1 188 GLY n 1 189 VAL n 1 190 ARG n 1 191 TYR n 1 192 SER n 1 193 SER n 1 194 PRO n 1 195 ALA n 1 196 ASN n 1 197 LEU n 1 198 TYR n 1 199 VAL n 1 200 ARG n 1 201 VAL n 1 202 GLN n 1 203 ASN n 1 204 VAL n 1 205 ALA n 1 206 PRO n 1 207 ARG n 1 208 PHE n 1 209 SER n 1 210 ILE n 1 211 LEU n 1 212 PRO n 1 213 MET n 1 214 SER n 1 215 HIS n 1 216 GLU n 1 217 ILE n 1 218 MET n 1 219 PRO n 1 220 GLY n 1 221 GLY n 1 222 ASN n 1 223 VAL n 1 224 ASN n 1 225 ILE n 1 226 THR n 1 227 CYS n 1 228 VAL n 1 229 ALA n 1 230 VAL n 1 231 GLY n 1 232 SER n 1 233 PRO n 1 234 MET n 1 235 PRO n 1 236 TYR n 1 237 VAL n 1 238 LYS n 1 239 TRP n 1 240 MET n 1 241 GLN n 1 242 GLY n 1 243 ALA n 1 244 GLU n 1 245 ASP n 1 246 LEU n 1 247 THR n 1 248 PRO n 1 249 GLU n 1 250 ASP n 1 251 ASP n 1 252 MET n 1 253 PRO n 1 254 VAL n 1 255 GLY n 1 256 ARG n 1 257 ASN n 1 258 VAL n 1 259 LEU n 1 260 GLU n 1 261 LEU n 1 262 THR n 1 263 ASP n 1 264 VAL n 1 265 LYS n 1 266 ASP n 1 267 SER n 1 268 ALA n 1 269 ASN n 1 270 TYR n 1 271 THR n 1 272 CYS n 1 273 VAL n 1 274 ALA n 1 275 MET n 1 276 SER n 1 277 SER n 1 278 LEU n 1 279 GLY n 1 280 VAL n 1 281 ILE n 1 282 GLU n 1 283 ALA n 1 284 VAL n 1 285 ALA n 1 286 GLN n 1 287 ILE n 1 288 THR n 1 289 VAL n 1 290 LYS n 1 291 SER n 1 292 LEU n 1 293 PRO n 1 294 LYS n 1 295 ALA n 1 296 GLY n 1 297 THR n 1 298 LYS n 1 299 HIS n 1 300 HIS n 1 301 HIS n 1 302 HIS n 1 303 HIS n 1 304 HIS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _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 HUMAN _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 'HOMO SAPIENS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 HUMAN _entity_src_gen.pdbx_host_org_scientific_name 'HOMO SAPIENS' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 9606 _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 HEK293T _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 PLASMID _entity_src_gen.pdbx_host_org_vector PHLSEC _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 ? # 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 B3P non-polymer . '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' ? 'C11 H26 N2 O6' 282.334 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 IOD non-polymer . 'IODIDE ION' ? 'I -1' 126.904 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 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 GLU 1 27 ? ? ? A . n A 1 2 THR 2 28 ? ? ? A . n A 1 3 GLY 3 29 ? ? ? A . n A 1 4 GLU 4 30 30 GLU GLU A . n A 1 5 GLU 5 31 31 GLU GLU A . n A 1 6 PRO 6 32 32 PRO PRO A . n A 1 7 PRO 7 33 33 PRO PRO A . n A 1 8 ARG 8 34 34 ARG ARG A . n A 1 9 PHE 9 35 35 PHE PHE A . n A 1 10 ILE 10 36 36 ILE ILE A . n A 1 11 LYS 11 37 37 LYS LYS A . n A 1 12 GLU 12 38 38 GLU GLU A . n A 1 13 PRO 13 39 39 PRO PRO A . n A 1 14 LYS 14 40 40 LYS LYS A . n A 1 15 ASP 15 41 41 ASP ASP A . n A 1 16 GLN 16 42 42 GLN GLN A . n A 1 17 ILE 17 43 43 ILE ILE A . n A 1 18 GLY 18 44 44 GLY GLY A . n A 1 19 VAL 19 45 45 VAL VAL A . n A 1 20 SER 20 46 46 SER SER A . n A 1 21 GLY 21 47 47 GLY GLY A . n A 1 22 GLY 22 48 48 GLY GLY A . n A 1 23 VAL 23 49 49 VAL VAL A . n A 1 24 ALA 24 50 50 ALA ALA A . n A 1 25 SER 25 51 51 SER SER A . n A 1 26 PHE 26 52 52 PHE PHE A . n A 1 27 VAL 27 53 53 VAL VAL A . n A 1 28 CYS 28 54 54 CYS CYS A . n A 1 29 GLN 29 55 55 GLN GLN A . n A 1 30 ALA 30 56 56 ALA ALA A . n A 1 31 THR 31 57 57 THR THR A . n A 1 32 GLY 32 58 58 GLY GLY A . n A 1 33 ASP 33 59 59 ASP ASP A . n A 1 34 PRO 34 60 60 PRO PRO A . n A 1 35 LYS 35 61 61 LYS LYS A . n A 1 36 PRO 36 62 62 PRO PRO A . n A 1 37 ARG 37 63 63 ARG ARG A . n A 1 38 VAL 38 64 64 VAL VAL A . n A 1 39 THR 39 65 65 THR THR A . n A 1 40 TRP 40 66 66 TRP TRP A . n A 1 41 ASN 41 67 67 ASN ASN A . n A 1 42 LYS 42 68 ? ? ? A . n A 1 43 LYS 43 69 ? ? ? A . n A 1 44 GLY 44 70 ? ? ? A . n A 1 45 LYS 45 71 ? ? ? A . n A 1 46 LYS 46 72 ? ? ? A . n A 1 47 VAL 47 73 ? ? ? A . n A 1 48 ASN 48 74 ? ? ? A . n A 1 49 SER 49 75 75 SER SER A . n A 1 50 GLN 50 76 76 GLN GLN A . n A 1 51 ARG 51 77 77 ARG ARG A . n A 1 52 PHE 52 78 78 PHE PHE A . n A 1 53 GLU 53 79 79 GLU GLU A . n A 1 54 THR 54 80 80 THR THR A . n A 1 55 ILE 55 81 81 ILE ILE A . n A 1 56 GLU 56 82 82 GLU GLU A . n A 1 57 PHE 57 83 83 PHE PHE A . n A 1 58 ASP 58 84 84 ASP ASP A . n A 1 59 GLU 59 85 85 GLU GLU A . n A 1 60 SER 60 86 86 SER SER A . n A 1 61 ALA 61 87 87 ALA ALA A . n A 1 62 GLY 62 88 88 GLY GLY A . n A 1 63 ALA 63 89 89 ALA ALA A . n A 1 64 VAL 64 90 90 VAL VAL A . n A 1 65 LEU 65 91 91 LEU LEU A . n A 1 66 ARG 66 92 92 ARG ARG A . n A 1 67 ILE 67 93 93 ILE ILE A . n A 1 68 GLN 68 94 94 GLN GLN A . n A 1 69 PRO 69 95 95 PRO PRO A . n A 1 70 LEU 70 96 96 LEU LEU A . n A 1 71 ARG 71 97 97 ARG ARG A . n A 1 72 THR 72 98 98 THR THR A . n A 1 73 PRO 73 99 99 PRO PRO A . n A 1 74 ARG 74 100 100 ARG ARG A . n A 1 75 ASP 75 101 101 ASP ASP A . n A 1 76 GLU 76 102 102 GLU GLU A . n A 1 77 ASN 77 103 103 ASN ASN A . n A 1 78 VAL 78 104 104 VAL VAL A . n A 1 79 TYR 79 105 105 TYR TYR A . n A 1 80 GLU 80 106 106 GLU GLU A . n A 1 81 CYS 81 107 107 CYS CYS A . n A 1 82 VAL 82 108 108 VAL VAL A . n A 1 83 ALA 83 109 109 ALA ALA A . n A 1 84 GLN 84 110 110 GLN GLN A . n A 1 85 ASN 85 111 111 ASN ASN A . n A 1 86 SER 86 112 112 SER SER A . n A 1 87 VAL 87 113 113 VAL VAL A . n A 1 88 GLY 88 114 114 GLY GLY A . n A 1 89 GLU 89 115 115 GLU GLU A . n A 1 90 ILE 90 116 116 ILE ILE A . n A 1 91 THR 91 117 117 THR THR A . n A 1 92 VAL 92 118 118 VAL VAL A . n A 1 93 HIS 93 119 119 HIS HIS A . n A 1 94 ALA 94 120 120 ALA ALA A . n A 1 95 LYS 95 121 121 LYS LYS A . n A 1 96 LEU 96 122 122 LEU LEU A . n A 1 97 THR 97 123 123 THR THR A . n A 1 98 VAL 98 124 124 VAL VAL A . n A 1 99 LEU 99 125 125 LEU LEU A . n A 1 100 ARG 100 126 126 ARG ARG A . n A 1 101 GLU 101 127 127 GLU GLU A . n A 1 102 ASP 102 128 128 ASP ASP A . n A 1 103 GLN 103 129 129 GLN GLN A . n A 1 104 LEU 104 130 130 LEU LEU A . n A 1 105 PRO 105 131 131 PRO PRO A . n A 1 106 SER 106 132 132 SER SER A . n A 1 107 GLY 107 133 133 GLY GLY A . n A 1 108 PHE 108 134 134 PHE PHE A . n A 1 109 PRO 109 135 135 PRO PRO A . n A 1 110 ASN 110 136 136 ASN ASN A . n A 1 111 ILE 111 137 137 ILE ILE A . n A 1 112 ASP 112 138 138 ASP ASP A . n A 1 113 MET 113 139 139 MET MET A . n A 1 114 GLY 114 140 140 GLY GLY A . n A 1 115 PRO 115 141 141 PRO PRO A . n A 1 116 GLN 116 142 142 GLN GLN A . n A 1 117 LEU 117 143 143 LEU LEU A . n A 1 118 LYS 118 144 144 LYS LYS A . n A 1 119 VAL 119 145 145 VAL VAL A . n A 1 120 VAL 120 146 146 VAL VAL A . n A 1 121 GLU 121 147 147 GLU GLU A . n A 1 122 ARG 122 148 148 ARG ARG A . n A 1 123 THR 123 149 149 THR THR A . n A 1 124 ARG 124 150 150 ARG ARG A . n A 1 125 THR 125 151 151 THR THR A . n A 1 126 ALA 126 152 152 ALA ALA A . n A 1 127 THR 127 153 153 THR THR A . n A 1 128 MET 128 154 154 MET MET A . n A 1 129 LEU 129 155 155 LEU LEU A . n A 1 130 CYS 130 156 156 CYS CYS A . n A 1 131 ALA 131 157 157 ALA ALA A . n A 1 132 ALA 132 158 158 ALA ALA A . n A 1 133 SER 133 159 159 SER SER A . n A 1 134 GLY 134 160 160 GLY GLY A . n A 1 135 ASN 135 161 161 ASN ASN A . n A 1 136 PRO 136 162 162 PRO PRO A . n A 1 137 ASP 137 163 163 ASP ASP A . n A 1 138 PRO 138 164 164 PRO PRO A . n A 1 139 GLU 139 165 165 GLU GLU A . n A 1 140 ILE 140 166 166 ILE ILE A . n A 1 141 THR 141 167 167 THR THR A . n A 1 142 TRP 142 168 168 TRP TRP A . n A 1 143 PHE 143 169 169 PHE PHE A . n A 1 144 LYS 144 170 170 LYS LYS A . n A 1 145 ASP 145 171 171 ASP ASP A . n A 1 146 PHE 146 172 172 PHE PHE A . n A 1 147 LEU 147 173 173 LEU LEU A . n A 1 148 PRO 148 174 174 PRO PRO A . n A 1 149 VAL 149 175 175 VAL VAL A . n A 1 150 ASP 150 176 176 ASP ASP A . n A 1 151 PRO 151 177 177 PRO PRO A . n A 1 152 SER 152 178 178 SER SER A . n A 1 153 ALA 153 179 179 ALA ALA A . n A 1 154 SER 154 180 180 SER SER A . n A 1 155 ASN 155 181 181 ASN ASN A . n A 1 156 GLY 156 182 182 GLY GLY A . n A 1 157 ARG 157 183 183 ARG ARG A . n A 1 158 ILE 158 184 184 ILE ILE A . n A 1 159 LYS 159 185 185 LYS LYS A . n A 1 160 GLN 160 186 186 GLN GLN A . n A 1 161 LEU 161 187 187 LEU LEU A . n A 1 162 ARG 162 188 188 ARG ARG A . n A 1 163 SER 163 189 189 SER SER A . n A 1 164 GLY 164 190 190 GLY GLY A . n A 1 165 ALA 165 191 191 ALA ALA A . n A 1 166 LEU 166 192 192 LEU LEU A . n A 1 167 GLN 167 193 193 GLN GLN A . n A 1 168 ILE 168 194 194 ILE ILE A . n A 1 169 GLU 169 195 195 GLU GLU A . n A 1 170 SER 170 196 196 SER SER A . n A 1 171 SER 171 197 197 SER SER A . n A 1 172 GLU 172 198 198 GLU GLU A . n A 1 173 GLU 173 199 199 GLU GLU A . n A 1 174 THR 174 200 200 THR THR A . n A 1 175 ASP 175 201 201 ASP ASP A . n A 1 176 GLN 176 202 202 GLN GLN A . n A 1 177 GLY 177 203 203 GLY GLY A . n A 1 178 LYS 178 204 204 LYS LYS A . n A 1 179 TYR 179 205 205 TYR TYR A . n A 1 180 GLU 180 206 206 GLU GLU A . n A 1 181 CYS 181 207 207 CYS CYS A . n A 1 182 VAL 182 208 208 VAL VAL A . n A 1 183 ALA 183 209 209 ALA ALA A . n A 1 184 THR 184 210 210 THR THR A . n A 1 185 ASN 185 211 211 ASN ASN A . n A 1 186 SER 186 212 212 SER SER A . n A 1 187 ALA 187 213 213 ALA ALA A . n A 1 188 GLY 188 214 214 GLY GLY A . n A 1 189 VAL 189 215 215 VAL VAL A . n A 1 190 ARG 190 216 216 ARG ARG A . n A 1 191 TYR 191 217 217 TYR TYR A . n A 1 192 SER 192 218 218 SER SER A . n A 1 193 SER 193 219 219 SER SER A . n A 1 194 PRO 194 220 220 PRO PRO A . n A 1 195 ALA 195 221 221 ALA ALA A . n A 1 196 ASN 196 222 222 ASN ASN A . n A 1 197 LEU 197 223 223 LEU LEU A . n A 1 198 TYR 198 224 224 TYR TYR A . n A 1 199 VAL 199 225 225 VAL VAL A . n A 1 200 ARG 200 226 226 ARG ARG A . n A 1 201 VAL 201 227 227 VAL VAL A . n A 1 202 GLN 202 228 228 GLN GLN A . n A 1 203 ASN 203 229 229 ASN ASN A . n A 1 204 VAL 204 230 230 VAL VAL A . n A 1 205 ALA 205 231 231 ALA ALA A . n A 1 206 PRO 206 232 232 PRO PRO A . n A 1 207 ARG 207 233 233 ARG ARG A . n A 1 208 PHE 208 234 234 PHE PHE A . n A 1 209 SER 209 235 235 SER SER A . n A 1 210 ILE 210 236 236 ILE ILE A . n A 1 211 LEU 211 237 237 LEU LEU A . n A 1 212 PRO 212 238 238 PRO PRO A . n A 1 213 MET 213 239 239 MET MET A . n A 1 214 SER 214 240 240 SER SER A . n A 1 215 HIS 215 241 241 HIS HIS A . n A 1 216 GLU 216 242 242 GLU GLU A . n A 1 217 ILE 217 243 243 ILE ILE A . n A 1 218 MET 218 244 244 MET MET A . n A 1 219 PRO 219 245 245 PRO PRO A . n A 1 220 GLY 220 246 246 GLY GLY A . n A 1 221 GLY 221 247 247 GLY GLY A . n A 1 222 ASN 222 248 248 ASN ASN A . n A 1 223 VAL 223 249 249 VAL VAL A . n A 1 224 ASN 224 250 250 ASN ASN A . n A 1 225 ILE 225 251 251 ILE ILE A . n A 1 226 THR 226 252 252 THR THR A . n A 1 227 CYS 227 253 253 CYS CYS A . n A 1 228 VAL 228 254 254 VAL VAL A . n A 1 229 ALA 229 255 255 ALA ALA A . n A 1 230 VAL 230 256 256 VAL VAL A . n A 1 231 GLY 231 257 257 GLY GLY A . n A 1 232 SER 232 258 258 SER SER A . n A 1 233 PRO 233 259 259 PRO PRO A . n A 1 234 MET 234 260 260 MET MET A . n A 1 235 PRO 235 261 261 PRO PRO A . n A 1 236 TYR 236 262 262 TYR TYR A . n A 1 237 VAL 237 263 263 VAL VAL A . n A 1 238 LYS 238 264 264 LYS LYS A . n A 1 239 TRP 239 265 265 TRP TRP A . n A 1 240 MET 240 266 266 MET MET A . n A 1 241 GLN 241 267 267 GLN GLN A . n A 1 242 GLY 242 268 268 GLY GLY A . n A 1 243 ALA 243 269 269 ALA ALA A . n A 1 244 GLU 244 270 270 GLU GLU A . n A 1 245 ASP 245 271 271 ASP ASP A . n A 1 246 LEU 246 272 272 LEU LEU A . n A 1 247 THR 247 273 273 THR THR A . n A 1 248 PRO 248 274 274 PRO PRO A . n A 1 249 GLU 249 275 275 GLU GLU A . n A 1 250 ASP 250 276 276 ASP ASP A . n A 1 251 ASP 251 277 277 ASP ASP A . n A 1 252 MET 252 278 278 MET MET A . n A 1 253 PRO 253 279 279 PRO PRO A . n A 1 254 VAL 254 280 280 VAL VAL A . n A 1 255 GLY 255 281 281 GLY GLY A . n A 1 256 ARG 256 282 282 ARG ARG A . n A 1 257 ASN 257 283 283 ASN ASN A . n A 1 258 VAL 258 284 284 VAL VAL A . n A 1 259 LEU 259 285 285 LEU LEU A . n A 1 260 GLU 260 286 286 GLU GLU A . n A 1 261 LEU 261 287 287 LEU LEU A . n A 1 262 THR 262 288 288 THR THR A . n A 1 263 ASP 263 289 289 ASP ASP A . n A 1 264 VAL 264 290 290 VAL VAL A . n A 1 265 LYS 265 291 291 LYS LYS A . n A 1 266 ASP 266 292 292 ASP ASP A . n A 1 267 SER 267 293 293 SER SER A . n A 1 268 ALA 268 294 294 ALA ALA A . n A 1 269 ASN 269 295 295 ASN ASN A . n A 1 270 TYR 270 296 296 TYR TYR A . n A 1 271 THR 271 297 297 THR THR A . n A 1 272 CYS 272 298 298 CYS CYS A . n A 1 273 VAL 273 299 299 VAL VAL A . n A 1 274 ALA 274 300 300 ALA ALA A . n A 1 275 MET 275 301 301 MET MET A . n A 1 276 SER 276 302 302 SER SER A . n A 1 277 SER 277 303 303 SER SER A . n A 1 278 LEU 278 304 304 LEU LEU A . n A 1 279 GLY 279 305 305 GLY GLY A . n A 1 280 VAL 280 306 306 VAL VAL A . n A 1 281 ILE 281 307 307 ILE ILE A . n A 1 282 GLU 282 308 308 GLU GLU A . n A 1 283 ALA 283 309 309 ALA ALA A . n A 1 284 VAL 284 310 310 VAL VAL A . n A 1 285 ALA 285 311 311 ALA ALA A . n A 1 286 GLN 286 312 312 GLN GLN A . n A 1 287 ILE 287 313 313 ILE ILE A . n A 1 288 THR 288 314 314 THR THR A . n A 1 289 VAL 289 315 ? ? ? A . n A 1 290 LYS 290 316 ? ? ? A . n A 1 291 SER 291 317 ? ? ? A . n A 1 292 LEU 292 318 ? ? ? A . n A 1 293 PRO 293 319 ? ? ? A . n A 1 294 LYS 294 320 ? ? ? A . n A 1 295 ALA 295 321 ? ? ? A . n A 1 296 GLY 296 322 ? ? ? A . n A 1 297 THR 297 323 ? ? ? A . n A 1 298 LYS 298 324 ? ? ? A . n A 1 299 HIS 299 325 ? ? ? A . n A 1 300 HIS 300 326 ? ? ? A . n A 1 301 HIS 301 327 ? ? ? A . n A 1 302 HIS 302 328 ? ? ? A . n A 1 303 HIS 303 329 ? ? ? A . n A 1 304 HIS 304 330 ? ? ? A . 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 B 2 CL 1 1315 1315 CL CL A . C 2 CL 1 1316 1316 CL CL A . D 2 CL 1 1317 1317 CL CL A . E 2 CL 1 1318 1318 CL CL A . F 3 IOD 1 1319 1319 IOD IOD A . G 3 IOD 1 1320 1320 IOD IOD A . H 3 IOD 1 1321 1321 IOD IOD A . I 3 IOD 1 1322 1322 IOD IOD A . J 4 NAG 1 1323 1323 NAG NAG A . K 4 NAG 1 1324 1324 NAG NAG A . L 5 B3P 1 1325 1325 B3P B3P A . M 6 HOH 1 2001 2001 HOH HOH A . M 6 HOH 2 2002 2002 HOH HOH A . M 6 HOH 3 2003 2003 HOH HOH A . M 6 HOH 4 2004 2004 HOH HOH A . M 6 HOH 5 2005 2005 HOH HOH A . M 6 HOH 6 2006 2006 HOH HOH A . M 6 HOH 7 2007 2007 HOH HOH A . M 6 HOH 8 2008 2008 HOH HOH A . M 6 HOH 9 2009 2009 HOH HOH A . M 6 HOH 10 2010 2010 HOH HOH A . M 6 HOH 11 2011 2011 HOH HOH A . M 6 HOH 12 2012 2012 HOH HOH A . M 6 HOH 13 2013 2013 HOH HOH A . M 6 HOH 14 2014 2014 HOH HOH A . M 6 HOH 15 2015 2015 HOH HOH A . M 6 HOH 16 2016 2016 HOH HOH A . M 6 HOH 17 2017 2017 HOH HOH A . M 6 HOH 18 2018 2018 HOH HOH A . M 6 HOH 19 2019 2019 HOH HOH A . M 6 HOH 20 2020 2020 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.6.0077 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 PHASER phasing . ? 4 # _cell.entry_id 2YD9 _cell.length_a 71.699 _cell.length_b 90.043 _cell.length_c 143.283 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YD9 _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 # _exptl.entry_id 2YD9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.48 _exptl_crystal.density_percent_sol 64.00 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '20% PEG 3350, 0.2 M SODIUM IODIDE, 0.1 M BIS-TRIS PROPANE, PH 7.5 .' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC CCD' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9786 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I04' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I04 _diffrn_source.pdbx_wavelength 0.9786 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2YD9 _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.00 _reflns.d_resolution_high 2.60 _reflns.number_obs 14979 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.13 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 14.60 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.2 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.60 _reflns_shell.d_res_low 2.70 _reflns_shell.percent_possible_all 99.9 _reflns_shell.Rmerge_I_obs 0.87 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.30 _reflns_shell.pdbx_redundancy 7.4 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2YD9 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 13846 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 44.16 _refine.ls_d_res_high 2.60 _refine.ls_percent_reflns_obs 99.5 _refine.ls_R_factor_obs 0.249 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.247 _refine.ls_R_factor_R_free 0.289 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.00 _refine.ls_number_reflns_R_free 736 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.918 _refine.correlation_coeff_Fo_to_Fc_free 0.886 _refine.B_iso_mean 59.20 _refine.aniso_B[1][1] -3.73 _refine.aniso_B[2][2] -4.91 _refine.aniso_B[3][3] 8.64 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CLEAR ELECTRON DENSITY WAS NOT VISIBLE FOR RESIDUES 68-74 AND THESE ARE NOT INCLUDED IN THE CRYSTAL STRUCTURE. ; _refine.pdbx_starting_model 'PDB ENTRY 2YD4' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.432 _refine.pdbx_overall_ESU_R_Free 0.305 _refine.overall_SU_ML 0.295 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 27.770 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2123 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 55 _refine_hist.number_atoms_solvent 20 _refine_hist.number_atoms_total 2198 _refine_hist.d_res_high 2.60 _refine_hist.d_res_low 44.16 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.006 0.022 ? 2216 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 1511 'X-RAY DIFFRACTION' ? r_angle_refined_deg 0.974 1.989 ? 3018 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.746 3.006 ? 3660 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.114 5.000 ? 276 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 38.241 24.896 ? 96 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 14.080 15.000 ? 356 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 12.962 15.000 ? 15 'X-RAY DIFFRACTION' ? r_chiral_restr 0.058 0.200 ? 344 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.003 0.021 ? 2443 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 399 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.60 _refine_ls_shell.d_res_low 2.67 _refine_ls_shell.number_reflns_R_work 1002 _refine_ls_shell.R_factor_R_work 0.3990 _refine_ls_shell.percent_reflns_obs 99.81 _refine_ls_shell.R_factor_R_free 0.4440 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 54 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2YD9 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2YD9 _struct.title 'Crystal structure of the N-terminal Ig1-3 module of Human Receptor Protein Tyrosine Phosphatase Sigma' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2YD9 _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text HYDROLASE # 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 2 ? D N N 2 ? E N N 2 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 4 ? K N N 4 ? L N N 5 ? M N N 6 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PTPRS_HUMAN _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession Q13332 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2YD9 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 295 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q13332 _struct_ref_seq.db_align_beg 30 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 321 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 30 _struct_ref_seq.pdbx_auth_seq_align_end 321 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2YD9 GLU A 1 ? UNP Q13332 ? ? 'expression tag' 27 1 1 2YD9 THR A 2 ? UNP Q13332 ? ? 'expression tag' 28 2 1 2YD9 GLY A 3 ? UNP Q13332 ? ? 'expression tag' 29 3 1 2YD9 GLN A 202 ? UNP Q13332 ARG 228 'engineered mutation' 228 4 1 2YD9 ASN A 203 ? UNP Q13332 ARG 229 'engineered mutation' 229 5 1 2YD9 GLY A 296 ? UNP Q13332 ? ? 'expression tag' 322 6 1 2YD9 THR A 297 ? UNP Q13332 ? ? 'expression tag' 323 7 1 2YD9 LYS A 298 ? UNP Q13332 ? ? 'expression tag' 324 8 1 2YD9 HIS A 299 ? UNP Q13332 ? ? 'expression tag' 325 9 1 2YD9 HIS A 300 ? UNP Q13332 ? ? 'expression tag' 326 10 1 2YD9 HIS A 301 ? UNP Q13332 ? ? 'expression tag' 327 11 1 2YD9 HIS A 302 ? UNP Q13332 ? ? 'expression tag' 328 12 1 2YD9 HIS A 303 ? UNP Q13332 ? ? 'expression tag' 329 13 1 2YD9 HIS A 304 ? UNP Q13332 ? ? 'expression tag' 330 14 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 5350 ? 1 MORE -68.3 ? 1 'SSA (A^2)' 30090 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_555 x,-y,-z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 # 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 1 ARG A 100 ? LEU A 104 ? ARG A 126 LEU A 130 5 ? 5 HELX_P HELX_P2 2 ASP A 150 ? ASN A 155 ? ASP A 176 ASN A 181 5 ? 6 HELX_P HELX_P3 3 GLU A 172 ? GLN A 176 ? GLU A 198 GLN A 202 5 ? 5 # _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 disulf1 disulf ? ? A CYS 28 SG ? ? ? 1_555 A CYS 81 SG ? ? A CYS 54 A CYS 107 1_555 ? ? ? ? ? ? ? 2.034 ? ? disulf2 disulf ? ? A CYS 130 SG ? ? ? 1_555 A CYS 181 SG ? ? A CYS 156 A CYS 207 1_555 ? ? ? ? ? ? ? 2.086 ? ? disulf3 disulf ? ? A CYS 227 SG ? ? ? 1_555 A CYS 272 SG ? ? A CYS 253 A CYS 298 1_555 ? ? ? ? ? ? ? 2.023 ? ? covale1 covale one ? A ASN 224 ND2 ? ? ? 1_555 K NAG . C1 ? ? A ASN 250 A NAG 1324 1_555 ? ? ? ? ? ? ? 1.444 ? N-Glycosylation covale2 covale one ? A ASN 269 ND2 ? ? ? 1_555 J NAG . C1 ? ? A ASN 295 A NAG 1323 1_555 ? ? ? ? ? ? ? 1.448 ? N-Glycosylation # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # loop_ _pdbx_modification_feature.ordinal _pdbx_modification_feature.label_comp_id _pdbx_modification_feature.label_asym_id _pdbx_modification_feature.label_seq_id _pdbx_modification_feature.label_alt_id _pdbx_modification_feature.modified_residue_label_comp_id _pdbx_modification_feature.modified_residue_label_asym_id _pdbx_modification_feature.modified_residue_label_seq_id _pdbx_modification_feature.modified_residue_label_alt_id _pdbx_modification_feature.auth_comp_id _pdbx_modification_feature.auth_asym_id _pdbx_modification_feature.auth_seq_id _pdbx_modification_feature.PDB_ins_code _pdbx_modification_feature.symmetry _pdbx_modification_feature.modified_residue_auth_comp_id _pdbx_modification_feature.modified_residue_auth_asym_id _pdbx_modification_feature.modified_residue_auth_seq_id _pdbx_modification_feature.modified_residue_PDB_ins_code _pdbx_modification_feature.modified_residue_symmetry _pdbx_modification_feature.comp_id_linking_atom _pdbx_modification_feature.modified_residue_id_linking_atom _pdbx_modification_feature.modified_residue_id _pdbx_modification_feature.ref_pcm_id _pdbx_modification_feature.ref_comp_id _pdbx_modification_feature.type _pdbx_modification_feature.category 1 NAG J . ? ASN A 269 ? NAG A 1323 ? 1_555 ASN A 295 ? 1_555 C1 ND2 ASN 1 NAG N-Glycosylation Carbohydrate 2 NAG K . ? ASN A 224 ? NAG A 1324 ? 1_555 ASN A 250 ? 1_555 C1 ND2 ASN 1 NAG N-Glycosylation Carbohydrate 3 CYS A 28 ? CYS A 81 ? CYS A 54 ? 1_555 CYS A 107 ? 1_555 SG SG . . . None 'Disulfide bridge' 4 CYS A 130 ? CYS A 181 ? CYS A 156 ? 1_555 CYS A 207 ? 1_555 SG SG . . . None 'Disulfide bridge' 5 CYS A 227 ? CYS A 272 ? CYS A 253 ? 1_555 CYS A 298 ? 1_555 SG SG . . . None 'Disulfide bridge' # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 ASP 33 A . ? ASP 59 A PRO 34 A ? PRO 60 A 1 1.44 2 GLN 68 A . ? GLN 94 A PRO 69 A ? PRO 95 A 1 -9.56 3 THR 72 A . ? THR 98 A PRO 73 A ? PRO 99 A 1 -0.06 4 ASN 135 A . ? ASN 161 A PRO 136 A ? PRO 162 A 1 -1.17 5 GLY 220 A . ? GLY 246 A GLY 221 A ? GLY 247 A 1 0.89 6 SER 232 A . ? SER 258 A PRO 233 A ? PRO 259 A 1 6.10 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 4 ? AB ? 4 ? AC ? 4 ? AD ? 2 ? AE ? 2 ? AF ? 4 ? AG ? 5 ? AH ? 2 ? AI ? 3 ? AJ ? 3 ? AK ? 5 ? # 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 AA 1 2 ? anti-parallel AA 2 3 ? anti-parallel AA 3 4 ? anti-parallel AB 1 2 ? parallel AB 2 3 ? anti-parallel AB 3 4 ? parallel AC 1 2 ? parallel AC 2 3 ? anti-parallel AC 3 4 ? anti-parallel AD 1 2 ? parallel AE 1 2 ? anti-parallel AF 1 2 ? parallel AF 2 3 ? anti-parallel AF 3 4 ? parallel AG 1 2 ? parallel AG 2 3 ? anti-parallel AG 3 4 ? anti-parallel AG 4 5 ? anti-parallel AH 1 2 ? parallel AI 1 2 ? anti-parallel AI 2 3 ? anti-parallel AJ 1 2 ? anti-parallel AJ 2 3 ? anti-parallel AK 1 2 ? parallel AK 2 3 ? anti-parallel AK 3 4 ? anti-parallel AK 4 5 ? 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 AA 1 ARG A 8 ? LYS A 11 ? ARG A 34 LYS A 37 AA 2 ALA A 24 ? THR A 31 ? ALA A 50 THR A 57 AA 3 GLY A 62 ? ILE A 67 ? GLY A 88 ILE A 93 AA 4 PHE A 52 ? PHE A 57 ? PHE A 78 PHE A 83 AB 1 GLN A 16 ? VAL A 19 ? GLN A 42 VAL A 45 AB 2 HIS A 93 ? LEU A 99 ? HIS A 119 LEU A 125 AB 3 VAL A 78 ? GLN A 84 ? VAL A 104 GLN A 110 AB 4 GLU A 89 ? ILE A 90 ? GLU A 115 ILE A 116 AC 1 GLN A 16 ? VAL A 19 ? GLN A 42 VAL A 45 AC 2 HIS A 93 ? LEU A 99 ? HIS A 119 LEU A 125 AC 3 VAL A 78 ? GLN A 84 ? VAL A 104 GLN A 110 AC 4 ARG A 37 ? ASN A 41 ? ARG A 63 ASN A 67 AD 1 GLU A 89 ? ILE A 90 ? GLU A 115 ILE A 116 AD 2 VAL A 78 ? GLN A 84 ? VAL A 104 GLN A 110 AE 1 ASN A 110 ? MET A 113 ? ASN A 136 MET A 139 AE 2 ALA A 131 ? SER A 133 ? ALA A 157 SER A 159 AF 1 LYS A 118 ? GLU A 121 ? LYS A 144 GLU A 147 AF 2 ALA A 195 ? ARG A 200 ? ALA A 221 ARG A 226 AF 3 GLY A 177 ? ASN A 185 ? GLY A 203 ASN A 211 AF 4 GLY A 188 ? TYR A 191 ? GLY A 214 TYR A 217 AG 1 LYS A 118 ? GLU A 121 ? LYS A 144 GLU A 147 AG 2 ALA A 195 ? ARG A 200 ? ALA A 221 ARG A 226 AG 3 GLY A 177 ? ASN A 185 ? GLY A 203 ASN A 211 AG 4 GLU A 139 ? LYS A 144 ? GLU A 165 LYS A 170 AG 5 LEU A 147 ? PRO A 148 ? LEU A 173 PRO A 174 AH 1 GLY A 188 ? TYR A 191 ? GLY A 214 TYR A 217 AH 2 GLY A 177 ? ASN A 185 ? GLY A 203 ASN A 211 AI 1 ALA A 126 ? MET A 128 ? ALA A 152 MET A 154 AI 2 LEU A 166 ? ILE A 168 ? LEU A 192 ILE A 194 AI 3 ILE A 158 ? GLN A 160 ? ILE A 184 GLN A 186 AJ 1 VAL A 204 ? ILE A 210 ? VAL A 230 ILE A 236 AJ 2 VAL A 223 ? SER A 232 ? VAL A 249 SER A 258 AJ 3 ARG A 256 ? LEU A 261 ? ARG A 282 LEU A 287 AK 1 HIS A 215 ? GLU A 216 ? HIS A 241 GLU A 242 AK 2 GLY A 279 ? THR A 288 ? GLY A 305 THR A 314 AK 3 ALA A 268 ? SER A 276 ? ALA A 294 SER A 302 AK 4 TYR A 236 ? GLN A 241 ? TYR A 262 GLN A 267 AK 5 GLU A 244 ? ASP A 245 ? GLU A 270 ASP A 271 # 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 AA 1 2 N LYS A 11 ? N LYS A 37 O GLN A 29 ? O GLN A 55 AA 2 3 N CYS A 28 ? N CYS A 54 O ALA A 63 ? O ALA A 89 AA 3 4 N ARG A 66 ? N ARG A 92 O GLU A 53 ? O GLU A 79 AB 1 2 N GLN A 16 ? N GLN A 42 O LYS A 95 ? O LYS A 121 AB 2 3 N ALA A 94 ? N ALA A 120 O TYR A 79 ? O TYR A 105 AB 3 4 N ALA A 83 ? N ALA A 109 O ILE A 90 ? O ILE A 116 AC 1 2 N GLN A 16 ? N GLN A 42 O LYS A 95 ? O LYS A 121 AC 2 3 N ALA A 94 ? N ALA A 120 O TYR A 79 ? O TYR A 105 AC 3 4 N GLN A 84 ? N GLN A 110 O ARG A 37 ? O ARG A 63 AD 1 2 N ILE A 90 ? N ILE A 116 O ALA A 83 ? O ALA A 109 AE 1 2 N MET A 113 ? N MET A 139 O ALA A 131 ? O ALA A 157 AF 1 2 N LYS A 118 ? N LYS A 144 O ASN A 196 ? O ASN A 222 AF 2 3 N LEU A 197 ? N LEU A 223 O GLY A 177 ? O GLY A 203 AF 3 4 N ASN A 185 ? N ASN A 211 O GLY A 188 ? O GLY A 214 AG 1 2 N LYS A 118 ? N LYS A 144 O ASN A 196 ? O ASN A 222 AG 2 3 N LEU A 197 ? N LEU A 223 O GLY A 177 ? O GLY A 203 AG 3 4 N THR A 184 ? N THR A 210 O GLU A 139 ? O GLU A 165 AG 4 5 N LYS A 144 ? N LYS A 170 O LEU A 147 ? O LEU A 173 AH 1 2 N ARG A 190 ? N ARG A 216 O ALA A 183 ? O ALA A 209 AI 1 2 N MET A 128 ? N MET A 154 O LEU A 166 ? O LEU A 192 AI 2 3 N GLN A 167 ? N GLN A 193 O LYS A 159 ? O LYS A 185 AJ 1 2 N SER A 209 ? N SER A 235 O VAL A 228 ? O VAL A 254 AJ 2 3 N CYS A 227 ? N CYS A 253 O ASN A 257 ? O ASN A 283 AK 1 2 N HIS A 215 ? N HIS A 241 O GLN A 286 ? O GLN A 312 AK 2 3 N ILE A 287 ? N ILE A 313 O ALA A 268 ? O ALA A 294 AK 3 4 N MET A 275 ? N MET A 301 O TYR A 236 ? O TYR A 262 AK 4 5 N GLN A 241 ? N GLN A 267 O GLU A 244 ? O GLU A 270 # _pdbx_entry_details.entry_id 2YD9 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) DERIVE FROM THE PHLSEC VECTOR. THE R228Q AND R229N POINT MUTATIONS WERE INTRODUCED TO PREVENT PROTEOLYTIC CLEAVAGE OF THE PROTEIN. ; _pdbx_entry_details.has_ligand_of_interest ? _pdbx_entry_details.has_protein_modification Y # 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 CYS A 54 ? ? -165.68 109.71 2 1 SER A 86 ? ? 84.42 -14.78 3 1 LEU A 143 ? ? -39.10 126.62 4 1 THR A 149 ? ? 75.38 -9.21 5 1 CYS A 156 ? ? -164.63 113.01 6 1 ASN A 229 ? ? -145.01 52.37 7 1 THR A 288 ? ? -81.25 -76.70 # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A ASN 224 A ASN 250 ? ASN 'GLYCOSYLATION SITE' 2 A ASN 269 A ASN 295 ? ASN 'GLYCOSYLATION SITE' # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id IOD _pdbx_struct_special_symmetry.auth_seq_id 1319 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id F _pdbx_struct_special_symmetry.label_comp_id IOD _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -33.5113 -23.8646 -30.8818 0.9479 0.7281 0.2164 0.1414 0.0332 -0.1411 6.0843 11.7653 4.2762 0.7456 -1.4569 -3.7735 0.2701 1.3959 -0.3424 -1.7982 -0.2016 -0.6251 0.3761 0.6187 -0.0684 'X-RAY DIFFRACTION' 2 ? refined -37.7439 -19.3642 -10.4949 0.1313 0.0812 0.0624 -0.0118 -0.0476 -0.0008 3.7401 6.4342 1.7081 -1.4780 -0.3912 0.6972 0.0853 0.2266 0.0620 -0.4527 0.0004 -0.2486 0.0841 0.0085 -0.0857 'X-RAY DIFFRACTION' 3 ? refined -64.4506 12.9783 8.9948 0.2822 0.5464 0.1508 -0.1881 0.0242 -0.1145 14.4102 5.0306 6.9837 -4.9872 -5.0503 1.7081 0.2758 -1.6584 0.3989 0.8077 -0.2224 0.0099 -0.4341 -0.3371 -0.0534 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 30 ? ? A 128 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 129 ? ? A 226 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 227 ? ? A 314 ? ? ? ? # 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 A GLU 27 ? A GLU 1 2 1 Y 1 A THR 28 ? A THR 2 3 1 Y 1 A GLY 29 ? A GLY 3 4 1 Y 1 A LYS 68 ? A LYS 42 5 1 Y 1 A LYS 69 ? A LYS 43 6 1 Y 1 A GLY 70 ? A GLY 44 7 1 Y 1 A LYS 71 ? A LYS 45 8 1 Y 1 A LYS 72 ? A LYS 46 9 1 Y 1 A VAL 73 ? A VAL 47 10 1 Y 1 A ASN 74 ? A ASN 48 11 1 Y 1 A VAL 315 ? A VAL 289 12 1 Y 1 A LYS 316 ? A LYS 290 13 1 Y 1 A SER 317 ? A SER 291 14 1 Y 1 A LEU 318 ? A LEU 292 15 1 Y 1 A PRO 319 ? A PRO 293 16 1 Y 1 A LYS 320 ? A LYS 294 17 1 Y 1 A ALA 321 ? A ALA 295 18 1 Y 1 A GLY 322 ? A GLY 296 19 1 Y 1 A THR 323 ? A THR 297 20 1 Y 1 A LYS 324 ? A LYS 298 21 1 Y 1 A HIS 325 ? A HIS 299 22 1 Y 1 A HIS 326 ? A HIS 300 23 1 Y 1 A HIS 327 ? A HIS 301 24 1 Y 1 A HIS 328 ? A HIS 302 25 1 Y 1 A HIS 329 ? A HIS 303 26 1 Y 1 A HIS 330 ? A HIS 304 # 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 B3P C1 C N N 74 B3P C2 C N N 75 B3P C3 C N N 76 B3P N1 N N N 77 B3P C4 C N N 78 B3P C5 C N N 79 B3P C6 C N N 80 B3P C7 C N N 81 B3P N2 N N N 82 B3P C8 C N N 83 B3P C9 C N N 84 B3P C10 C N N 85 B3P C11 C N N 86 B3P O1 O N N 87 B3P O2 O N N 88 B3P O3 O N N 89 B3P O4 O N N 90 B3P O5 O N N 91 B3P O6 O N N 92 B3P H11 H N N 93 B3P H12 H N N 94 B3P H21 H N N 95 B3P H22 H N N 96 B3P H31 H N N 97 B3P H32 H N N 98 B3P HN1 H N N 99 B3P H51 H N N 100 B3P H52 H N N 101 B3P H61 H N N 102 B3P H62 H N N 103 B3P H71 H N N 104 B3P H72 H N N 105 B3P HN2 H N N 106 B3P H91 H N N 107 B3P H92 H N N 108 B3P H101 H N N 109 B3P H102 H N N 110 B3P H111 H N N 111 B3P H112 H N N 112 B3P HO1 H N N 113 B3P HO2 H N N 114 B3P HO3 H N N 115 B3P HO4 H N N 116 B3P HO5 H N N 117 B3P HO6 H N N 118 CL CL CL N N 119 CYS N N N N 120 CYS CA C N R 121 CYS C C N N 122 CYS O O N N 123 CYS CB C N N 124 CYS SG S N N 125 CYS OXT O N N 126 CYS H H N N 127 CYS H2 H N N 128 CYS HA H N N 129 CYS HB2 H N N 130 CYS HB3 H N N 131 CYS HG H N N 132 CYS HXT H N N 133 GLN N N N N 134 GLN CA C N S 135 GLN C C N N 136 GLN O O N N 137 GLN CB C N N 138 GLN CG C N N 139 GLN CD C N N 140 GLN OE1 O N N 141 GLN NE2 N N N 142 GLN OXT O N N 143 GLN H H N N 144 GLN H2 H N N 145 GLN HA H N N 146 GLN HB2 H N N 147 GLN HB3 H N N 148 GLN HG2 H N N 149 GLN HG3 H N N 150 GLN HE21 H N N 151 GLN HE22 H N N 152 GLN HXT H N N 153 GLU N N N N 154 GLU CA C N S 155 GLU C C N N 156 GLU O O N N 157 GLU CB C N N 158 GLU CG C N N 159 GLU CD C N N 160 GLU OE1 O N N 161 GLU OE2 O N N 162 GLU OXT O N N 163 GLU H H N N 164 GLU H2 H N N 165 GLU HA H N N 166 GLU HB2 H N N 167 GLU HB3 H N N 168 GLU HG2 H N N 169 GLU HG3 H N N 170 GLU HE2 H N N 171 GLU HXT H N N 172 GLY N N N N 173 GLY CA C N N 174 GLY C C N N 175 GLY O O N N 176 GLY OXT O N N 177 GLY H H N N 178 GLY H2 H N N 179 GLY HA2 H N N 180 GLY HA3 H N N 181 GLY HXT H N N 182 HIS N N N N 183 HIS CA C N S 184 HIS C C N N 185 HIS O O N N 186 HIS CB C N N 187 HIS CG C Y N 188 HIS ND1 N Y N 189 HIS CD2 C Y N 190 HIS CE1 C Y N 191 HIS NE2 N Y N 192 HIS OXT O N N 193 HIS H H N N 194 HIS H2 H N N 195 HIS HA H N N 196 HIS HB2 H N N 197 HIS HB3 H N N 198 HIS HD1 H N N 199 HIS HD2 H N N 200 HIS HE1 H N N 201 HIS HE2 H N N 202 HIS HXT H N N 203 HOH O O N N 204 HOH H1 H N N 205 HOH H2 H N N 206 ILE N N N N 207 ILE CA C N S 208 ILE C C N N 209 ILE O O N N 210 ILE CB C N S 211 ILE CG1 C N N 212 ILE CG2 C N N 213 ILE CD1 C N N 214 ILE OXT O N N 215 ILE H H N N 216 ILE H2 H N N 217 ILE HA H N N 218 ILE HB H N N 219 ILE HG12 H N N 220 ILE HG13 H N N 221 ILE HG21 H N N 222 ILE HG22 H N N 223 ILE HG23 H N N 224 ILE HD11 H N N 225 ILE HD12 H N N 226 ILE HD13 H N N 227 ILE HXT H N N 228 IOD I I N N 229 LEU N N N N 230 LEU CA C N S 231 LEU C C N N 232 LEU O O N N 233 LEU CB C N N 234 LEU CG C N N 235 LEU CD1 C N N 236 LEU CD2 C N N 237 LEU OXT O N N 238 LEU H H N N 239 LEU H2 H N N 240 LEU HA H N N 241 LEU HB2 H N N 242 LEU HB3 H N N 243 LEU HG H N N 244 LEU HD11 H N N 245 LEU HD12 H N N 246 LEU HD13 H N N 247 LEU HD21 H N N 248 LEU HD22 H N N 249 LEU HD23 H N N 250 LEU HXT H N N 251 LYS N N N N 252 LYS CA C N S 253 LYS C C N N 254 LYS O O N N 255 LYS CB C N N 256 LYS CG C N N 257 LYS CD C N N 258 LYS CE C N N 259 LYS NZ N N N 260 LYS OXT O N N 261 LYS H H N N 262 LYS H2 H N N 263 LYS HA H N N 264 LYS HB2 H N N 265 LYS HB3 H N N 266 LYS HG2 H N N 267 LYS HG3 H N N 268 LYS HD2 H N N 269 LYS HD3 H N N 270 LYS HE2 H N N 271 LYS HE3 H N N 272 LYS HZ1 H N N 273 LYS HZ2 H N N 274 LYS HZ3 H N N 275 LYS HXT H N N 276 MET N N N N 277 MET CA C N S 278 MET C C N N 279 MET O O N N 280 MET CB C N N 281 MET CG C N N 282 MET SD S N N 283 MET CE C N N 284 MET OXT O N N 285 MET H H N N 286 MET H2 H N N 287 MET HA H N N 288 MET HB2 H N N 289 MET HB3 H N N 290 MET HG2 H N N 291 MET HG3 H N N 292 MET HE1 H N N 293 MET HE2 H N N 294 MET HE3 H N N 295 MET HXT H N N 296 NAG C1 C N R 297 NAG C2 C N R 298 NAG C3 C N R 299 NAG C4 C N S 300 NAG C5 C N R 301 NAG C6 C N N 302 NAG C7 C N N 303 NAG C8 C N N 304 NAG N2 N N N 305 NAG O1 O N N 306 NAG O3 O N N 307 NAG O4 O N N 308 NAG O5 O N N 309 NAG O6 O N N 310 NAG O7 O N N 311 NAG H1 H N N 312 NAG H2 H N N 313 NAG H3 H N N 314 NAG H4 H N N 315 NAG H5 H N N 316 NAG H61 H N N 317 NAG H62 H N N 318 NAG H81 H N N 319 NAG H82 H N N 320 NAG H83 H N N 321 NAG HN2 H N N 322 NAG HO1 H N N 323 NAG HO3 H N N 324 NAG HO4 H N N 325 NAG HO6 H N N 326 PHE N N N N 327 PHE CA C N S 328 PHE C C N N 329 PHE O O N N 330 PHE CB C N N 331 PHE CG C Y N 332 PHE CD1 C Y N 333 PHE CD2 C Y N 334 PHE CE1 C Y N 335 PHE CE2 C Y N 336 PHE CZ C Y N 337 PHE OXT O N N 338 PHE H H N N 339 PHE H2 H N N 340 PHE HA H N N 341 PHE HB2 H N N 342 PHE HB3 H N N 343 PHE HD1 H N N 344 PHE HD2 H N N 345 PHE HE1 H N N 346 PHE HE2 H N N 347 PHE HZ H N N 348 PHE HXT H N N 349 PRO N N N N 350 PRO CA C N S 351 PRO C C N N 352 PRO O O N N 353 PRO CB C N N 354 PRO CG C N N 355 PRO CD C N N 356 PRO OXT O N N 357 PRO H H N N 358 PRO HA H N N 359 PRO HB2 H N N 360 PRO HB3 H N N 361 PRO HG2 H N N 362 PRO HG3 H N N 363 PRO HD2 H N N 364 PRO HD3 H N N 365 PRO HXT H N N 366 SER N N N N 367 SER CA C N S 368 SER C C N N 369 SER O O N N 370 SER CB C N N 371 SER OG O N N 372 SER OXT O N N 373 SER H H N N 374 SER H2 H N N 375 SER HA H N N 376 SER HB2 H N N 377 SER HB3 H N N 378 SER HG H N N 379 SER HXT H N N 380 THR N N N N 381 THR CA C N S 382 THR C C N N 383 THR O O N N 384 THR CB C N R 385 THR OG1 O N N 386 THR CG2 C N N 387 THR OXT O N N 388 THR H H N N 389 THR H2 H N N 390 THR HA H N N 391 THR HB H N N 392 THR HG1 H N N 393 THR HG21 H N N 394 THR HG22 H N N 395 THR HG23 H N N 396 THR HXT H N N 397 TRP N N N N 398 TRP CA C N S 399 TRP C C N N 400 TRP O O N N 401 TRP CB C N N 402 TRP CG C Y N 403 TRP CD1 C Y N 404 TRP CD2 C Y N 405 TRP NE1 N Y N 406 TRP CE2 C Y N 407 TRP CE3 C Y N 408 TRP CZ2 C Y N 409 TRP CZ3 C Y N 410 TRP CH2 C Y N 411 TRP OXT O N N 412 TRP H H N N 413 TRP H2 H N N 414 TRP HA H N N 415 TRP HB2 H N N 416 TRP HB3 H N N 417 TRP HD1 H N N 418 TRP HE1 H N N 419 TRP HE3 H N N 420 TRP HZ2 H N N 421 TRP HZ3 H N N 422 TRP HH2 H N N 423 TRP HXT H N N 424 TYR N N N N 425 TYR CA C N S 426 TYR C C N N 427 TYR O O N N 428 TYR CB C N N 429 TYR CG C Y N 430 TYR CD1 C Y N 431 TYR CD2 C Y N 432 TYR CE1 C Y N 433 TYR CE2 C Y N 434 TYR CZ C Y N 435 TYR OH O N N 436 TYR OXT O N N 437 TYR H H N N 438 TYR H2 H N N 439 TYR HA H N N 440 TYR HB2 H N N 441 TYR HB3 H N N 442 TYR HD1 H N N 443 TYR HD2 H N N 444 TYR HE1 H N N 445 TYR HE2 H N N 446 TYR HH H N N 447 TYR HXT H N N 448 VAL N N N N 449 VAL CA C N S 450 VAL C C N N 451 VAL O O N N 452 VAL CB C N N 453 VAL CG1 C N N 454 VAL CG2 C N N 455 VAL OXT O N N 456 VAL H H N N 457 VAL H2 H N N 458 VAL HA H N N 459 VAL HB H N N 460 VAL HG11 H N N 461 VAL HG12 H N N 462 VAL HG13 H N N 463 VAL HG21 H N N 464 VAL HG22 H N N 465 VAL HG23 H N N 466 VAL HXT H N N 467 # 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 B3P C1 C2 sing N N 70 B3P C1 C3 sing N N 71 B3P C1 H11 sing N N 72 B3P C1 H12 sing N N 73 B3P C2 N2 sing N N 74 B3P C2 H21 sing N N 75 B3P C2 H22 sing N N 76 B3P C3 N1 sing N N 77 B3P C3 H31 sing N N 78 B3P C3 H32 sing N N 79 B3P N1 C4 sing N N 80 B3P N1 HN1 sing N N 81 B3P C4 C5 sing N N 82 B3P C4 C6 sing N N 83 B3P C4 C7 sing N N 84 B3P C5 O4 sing N N 85 B3P C5 H51 sing N N 86 B3P C5 H52 sing N N 87 B3P C6 O5 sing N N 88 B3P C6 H61 sing N N 89 B3P C6 H62 sing N N 90 B3P C7 O6 sing N N 91 B3P C7 H71 sing N N 92 B3P C7 H72 sing N N 93 B3P N2 C8 sing N N 94 B3P N2 HN2 sing N N 95 B3P C8 C9 sing N N 96 B3P C8 C10 sing N N 97 B3P C8 C11 sing N N 98 B3P C9 O1 sing N N 99 B3P C9 H91 sing N N 100 B3P C9 H92 sing N N 101 B3P C10 O2 sing N N 102 B3P C10 H101 sing N N 103 B3P C10 H102 sing N N 104 B3P C11 O3 sing N N 105 B3P C11 H111 sing N N 106 B3P C11 H112 sing N N 107 B3P O1 HO1 sing N N 108 B3P O2 HO2 sing N N 109 B3P O3 HO3 sing N N 110 B3P O4 HO4 sing N N 111 B3P O5 HO5 sing N N 112 B3P O6 HO6 sing N N 113 CYS N CA sing N N 114 CYS N H sing N N 115 CYS N H2 sing N N 116 CYS CA C sing N N 117 CYS CA CB sing N N 118 CYS CA HA sing N N 119 CYS C O doub N N 120 CYS C OXT sing N N 121 CYS CB SG sing N N 122 CYS CB HB2 sing N N 123 CYS CB HB3 sing N N 124 CYS SG HG sing N N 125 CYS OXT HXT sing N N 126 GLN N CA sing N N 127 GLN N H sing N N 128 GLN N H2 sing N N 129 GLN CA C sing N N 130 GLN CA CB sing N N 131 GLN CA HA sing N N 132 GLN C O doub N N 133 GLN C OXT sing N N 134 GLN CB CG sing N N 135 GLN CB HB2 sing N N 136 GLN CB HB3 sing N N 137 GLN CG CD sing N N 138 GLN CG HG2 sing N N 139 GLN CG HG3 sing N N 140 GLN CD OE1 doub N N 141 GLN CD NE2 sing N N 142 GLN NE2 HE21 sing N N 143 GLN NE2 HE22 sing N N 144 GLN OXT HXT sing N N 145 GLU N CA sing N N 146 GLU N H sing N N 147 GLU N H2 sing N N 148 GLU CA C sing N N 149 GLU CA CB sing N N 150 GLU CA HA sing N N 151 GLU C O doub N N 152 GLU C OXT sing N N 153 GLU CB CG sing N N 154 GLU CB HB2 sing N N 155 GLU CB HB3 sing N N 156 GLU CG CD sing N N 157 GLU CG HG2 sing N N 158 GLU CG HG3 sing N N 159 GLU CD OE1 doub N N 160 GLU CD OE2 sing N N 161 GLU OE2 HE2 sing N N 162 GLU OXT HXT sing N N 163 GLY N CA sing N N 164 GLY N H sing N N 165 GLY N H2 sing N N 166 GLY CA C sing N N 167 GLY CA HA2 sing N N 168 GLY CA HA3 sing N N 169 GLY C O doub N N 170 GLY C OXT sing N N 171 GLY OXT HXT sing N N 172 HIS N CA sing N N 173 HIS N H sing N N 174 HIS N H2 sing N N 175 HIS CA C sing N N 176 HIS CA CB sing N N 177 HIS CA HA sing N N 178 HIS C O doub N N 179 HIS C OXT sing N N 180 HIS CB CG sing N N 181 HIS CB HB2 sing N N 182 HIS CB HB3 sing N N 183 HIS CG ND1 sing Y N 184 HIS CG CD2 doub Y N 185 HIS ND1 CE1 doub Y N 186 HIS ND1 HD1 sing N N 187 HIS CD2 NE2 sing Y N 188 HIS CD2 HD2 sing N N 189 HIS CE1 NE2 sing Y N 190 HIS CE1 HE1 sing N N 191 HIS NE2 HE2 sing N N 192 HIS OXT HXT sing N N 193 HOH O H1 sing N N 194 HOH O H2 sing N N 195 ILE N CA sing N N 196 ILE N H sing N N 197 ILE N H2 sing N N 198 ILE CA C sing N N 199 ILE CA CB sing N N 200 ILE CA HA sing N N 201 ILE C O doub N N 202 ILE C OXT sing N N 203 ILE CB CG1 sing N N 204 ILE CB CG2 sing N N 205 ILE CB HB sing N N 206 ILE CG1 CD1 sing N N 207 ILE CG1 HG12 sing N N 208 ILE CG1 HG13 sing N N 209 ILE CG2 HG21 sing N N 210 ILE CG2 HG22 sing N N 211 ILE CG2 HG23 sing N N 212 ILE CD1 HD11 sing N N 213 ILE CD1 HD12 sing N N 214 ILE CD1 HD13 sing N N 215 ILE OXT HXT sing N N 216 LEU N CA sing N N 217 LEU N H sing N N 218 LEU N H2 sing N N 219 LEU CA C sing N N 220 LEU CA CB sing N N 221 LEU CA HA sing N N 222 LEU C O doub N N 223 LEU C OXT sing N N 224 LEU CB CG sing N N 225 LEU CB HB2 sing N N 226 LEU CB HB3 sing N N 227 LEU CG CD1 sing N N 228 LEU CG CD2 sing N N 229 LEU CG HG sing N N 230 LEU CD1 HD11 sing N N 231 LEU CD1 HD12 sing N N 232 LEU CD1 HD13 sing N N 233 LEU CD2 HD21 sing N N 234 LEU CD2 HD22 sing N N 235 LEU CD2 HD23 sing N N 236 LEU OXT HXT sing N N 237 LYS N CA sing N N 238 LYS N H sing N N 239 LYS N H2 sing N N 240 LYS CA C sing N N 241 LYS CA CB sing N N 242 LYS CA HA sing N N 243 LYS C O doub N N 244 LYS C OXT sing N N 245 LYS CB CG sing N N 246 LYS CB HB2 sing N N 247 LYS CB HB3 sing N N 248 LYS CG CD sing N N 249 LYS CG HG2 sing N N 250 LYS CG HG3 sing N N 251 LYS CD CE sing N N 252 LYS CD HD2 sing N N 253 LYS CD HD3 sing N N 254 LYS CE NZ sing N N 255 LYS CE HE2 sing N N 256 LYS CE HE3 sing N N 257 LYS NZ HZ1 sing N N 258 LYS NZ HZ2 sing N N 259 LYS NZ HZ3 sing N N 260 LYS OXT HXT sing N N 261 MET N CA sing N N 262 MET N H sing N N 263 MET N H2 sing N N 264 MET CA C sing N N 265 MET CA CB sing N N 266 MET CA HA sing N N 267 MET C O doub N N 268 MET C OXT sing N N 269 MET CB CG sing N N 270 MET CB HB2 sing N N 271 MET CB HB3 sing N N 272 MET CG SD sing N N 273 MET CG HG2 sing N N 274 MET CG HG3 sing N N 275 MET SD CE sing N N 276 MET CE HE1 sing N N 277 MET CE HE2 sing N N 278 MET CE HE3 sing N N 279 MET OXT HXT sing N N 280 NAG C1 C2 sing N N 281 NAG C1 O1 sing N N 282 NAG C1 O5 sing N N 283 NAG C1 H1 sing N N 284 NAG C2 C3 sing N N 285 NAG C2 N2 sing N N 286 NAG C2 H2 sing N N 287 NAG C3 C4 sing N N 288 NAG C3 O3 sing N N 289 NAG C3 H3 sing N N 290 NAG C4 C5 sing N N 291 NAG C4 O4 sing N N 292 NAG C4 H4 sing N N 293 NAG C5 C6 sing N N 294 NAG C5 O5 sing N N 295 NAG C5 H5 sing N N 296 NAG C6 O6 sing N N 297 NAG C6 H61 sing N N 298 NAG C6 H62 sing N N 299 NAG C7 C8 sing N N 300 NAG C7 N2 sing N N 301 NAG C7 O7 doub N N 302 NAG C8 H81 sing N N 303 NAG C8 H82 sing N N 304 NAG C8 H83 sing N N 305 NAG N2 HN2 sing N N 306 NAG O1 HO1 sing N N 307 NAG O3 HO3 sing N N 308 NAG O4 HO4 sing N N 309 NAG O6 HO6 sing N N 310 PHE N CA sing N N 311 PHE N H sing N N 312 PHE N H2 sing N N 313 PHE CA C sing N N 314 PHE CA CB sing N N 315 PHE CA HA sing N N 316 PHE C O doub N N 317 PHE C OXT sing N N 318 PHE CB CG sing N N 319 PHE CB HB2 sing N N 320 PHE CB HB3 sing N N 321 PHE CG CD1 doub Y N 322 PHE CG CD2 sing Y N 323 PHE CD1 CE1 sing Y N 324 PHE CD1 HD1 sing N N 325 PHE CD2 CE2 doub Y N 326 PHE CD2 HD2 sing N N 327 PHE CE1 CZ doub Y N 328 PHE CE1 HE1 sing N N 329 PHE CE2 CZ sing Y N 330 PHE CE2 HE2 sing N N 331 PHE CZ HZ sing N N 332 PHE OXT HXT sing N N 333 PRO N CA sing N N 334 PRO N CD sing N N 335 PRO N H sing N N 336 PRO CA C sing N N 337 PRO CA CB sing N N 338 PRO CA HA sing N N 339 PRO C O doub N N 340 PRO C OXT sing N N 341 PRO CB CG sing N N 342 PRO CB HB2 sing N N 343 PRO CB HB3 sing N N 344 PRO CG CD sing N N 345 PRO CG HG2 sing N N 346 PRO CG HG3 sing N N 347 PRO CD HD2 sing N N 348 PRO CD HD3 sing N N 349 PRO OXT HXT sing N N 350 SER N CA sing N N 351 SER N H sing N N 352 SER N H2 sing N N 353 SER CA C sing N N 354 SER CA CB sing N N 355 SER CA HA sing N N 356 SER C O doub N N 357 SER C OXT sing N N 358 SER CB OG sing N N 359 SER CB HB2 sing N N 360 SER CB HB3 sing N N 361 SER OG HG sing N N 362 SER OXT HXT sing N N 363 THR N CA sing N N 364 THR N H sing N N 365 THR N H2 sing N N 366 THR CA C sing N N 367 THR CA CB sing N N 368 THR CA HA sing N N 369 THR C O doub N N 370 THR C OXT sing N N 371 THR CB OG1 sing N N 372 THR CB CG2 sing N N 373 THR CB HB sing N N 374 THR OG1 HG1 sing N N 375 THR CG2 HG21 sing N N 376 THR CG2 HG22 sing N N 377 THR CG2 HG23 sing N N 378 THR OXT HXT sing N N 379 TRP N CA sing N N 380 TRP N H sing N N 381 TRP N H2 sing N N 382 TRP CA C sing N N 383 TRP CA CB sing N N 384 TRP CA HA sing N N 385 TRP C O doub N N 386 TRP C OXT sing N N 387 TRP CB CG sing N N 388 TRP CB HB2 sing N N 389 TRP CB HB3 sing N N 390 TRP CG CD1 doub Y N 391 TRP CG CD2 sing Y N 392 TRP CD1 NE1 sing Y N 393 TRP CD1 HD1 sing N N 394 TRP CD2 CE2 doub Y N 395 TRP CD2 CE3 sing Y N 396 TRP NE1 CE2 sing Y N 397 TRP NE1 HE1 sing N N 398 TRP CE2 CZ2 sing Y N 399 TRP CE3 CZ3 doub Y N 400 TRP CE3 HE3 sing N N 401 TRP CZ2 CH2 doub Y N 402 TRP CZ2 HZ2 sing N N 403 TRP CZ3 CH2 sing Y N 404 TRP CZ3 HZ3 sing N N 405 TRP CH2 HH2 sing N N 406 TRP OXT HXT sing N N 407 TYR N CA sing N N 408 TYR N H sing N N 409 TYR N H2 sing N N 410 TYR CA C sing N N 411 TYR CA CB sing N N 412 TYR CA HA sing N N 413 TYR C O doub N N 414 TYR C OXT sing N N 415 TYR CB CG sing N N 416 TYR CB HB2 sing N N 417 TYR CB HB3 sing N N 418 TYR CG CD1 doub Y N 419 TYR CG CD2 sing Y N 420 TYR CD1 CE1 sing Y N 421 TYR CD1 HD1 sing N N 422 TYR CD2 CE2 doub Y N 423 TYR CD2 HD2 sing N N 424 TYR CE1 CZ doub Y N 425 TYR CE1 HE1 sing N N 426 TYR CE2 CZ sing Y N 427 TYR CE2 HE2 sing N N 428 TYR CZ OH sing N N 429 TYR OH HH sing N N 430 TYR OXT HXT sing N N 431 VAL N CA sing N N 432 VAL N H sing N N 433 VAL N H2 sing N N 434 VAL CA C sing N N 435 VAL CA CB sing N N 436 VAL CA HA sing N N 437 VAL C O doub N N 438 VAL C OXT sing N N 439 VAL CB CG1 sing N N 440 VAL CB CG2 sing N N 441 VAL CB HB sing N N 442 VAL CG1 HG11 sing N N 443 VAL CG1 HG12 sing N N 444 VAL CG1 HG13 sing N N 445 VAL CG2 HG21 sing N N 446 VAL CG2 HG22 sing N N 447 VAL CG2 HG23 sing N N 448 VAL OXT HXT sing N N 449 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2YD4 _pdbx_initial_refinement_model.details 'PDB ENTRY 2YD4' # _atom_sites.entry_id 2YD9 _atom_sites.fract_transf_matrix[1][1] 0.013947 _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] 0.011106 _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] 0.006979 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CL I N O S # loop_