data_5VIJ # _model_server_result.job_id KaCL7ri36QeOQspLAGeNLQ _model_server_result.datetime_utc '2024-11-30 19:26:40' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5vij # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 5VIJ # _exptl.entry_id 5VIJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 75.067 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5VIJ _cell.length_a 54.886 _cell.length_b 87.158 _cell.length_c 122.254 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VIJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 28 A CYS 28 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 44 A CYS 44 1_555 A SG CYS 63 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf3 B SG CYS 29 B CYS 32 1_555 B SG CYS 55 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf4 B SG CYS 36 B CYS 39 1_555 B SG CYS 56 B CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf5 B SG CYS 226 B CYS 229 1_555 B SG CYS 281 B CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'C2 H5 N O2' _chem_comp.formula_weight 75.067 _chem_comp.id GLY _chem_comp.mon_nstd_flag y _chem_comp.name GLYCINE _chem_comp.type 'peptide linking' _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N CA GLY sing 154 n n N H GLY sing 155 n n N H2 GLY sing 156 n n CA C GLY sing 157 n n CA HA2 GLY sing 158 n n CA HA3 GLY sing 159 n n C O GLY doub 160 n n C OXT GLY sing 161 n n OXT HXT GLY sing 162 n n # _atom_sites.entry_id 5VIJ _atom_sites.fract_transf_matrix[1][1] 0.01822 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011473 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00818 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code C 3 GLY A 1 1001 1001 GLY GLY . D 4 5DX B 1 301 286 5DX ST1 . E 5 HOH A 1 1101 1081 HOH HOH . E 5 HOH A 2 1102 1089 HOH HOH . E 5 HOH A 3 1103 1055 HOH HOH . E 5 HOH A 4 1104 1044 HOH HOH . E 5 HOH A 5 1105 1109 HOH HOH . E 5 HOH A 6 1106 1110 HOH HOH . E 5 HOH A 7 1107 1119 HOH HOH . E 5 HOH A 8 1108 1070 HOH HOH . E 5 HOH A 9 1109 1061 HOH HOH . E 5 HOH A 10 1110 1048 HOH HOH . E 5 HOH A 11 1111 1080 HOH HOH . E 5 HOH A 12 1112 1026 HOH HOH . E 5 HOH A 13 1113 1106 HOH HOH . E 5 HOH A 14 1114 1111 HOH HOH . E 5 HOH A 15 1115 1096 HOH HOH . E 5 HOH A 16 1116 1095 HOH HOH . E 5 HOH A 17 1117 1015 HOH HOH . E 5 HOH A 18 1118 1047 HOH HOH . E 5 HOH A 19 1119 1113 HOH HOH . E 5 HOH A 20 1120 1082 HOH HOH . E 5 HOH A 21 1121 1065 HOH HOH . E 5 HOH A 22 1122 1051 HOH HOH . E 5 HOH A 23 1123 1049 HOH HOH . E 5 HOH A 24 1124 1066 HOH HOH . E 5 HOH A 25 1125 1072 HOH HOH . E 5 HOH A 26 1126 1033 HOH HOH . E 5 HOH A 27 1127 1050 HOH HOH . E 5 HOH A 28 1128 1012 HOH HOH . E 5 HOH A 29 1129 1027 HOH HOH . E 5 HOH A 30 1130 1010 HOH HOH . E 5 HOH A 31 1131 1046 HOH HOH . E 5 HOH A 32 1132 1101 HOH HOH . E 5 HOH A 33 1133 1076 HOH HOH . E 5 HOH A 34 1134 1069 HOH HOH . E 5 HOH A 35 1135 1023 HOH HOH . E 5 HOH A 36 1136 1100 HOH HOH . E 5 HOH A 37 1137 1032 HOH HOH . E 5 HOH A 38 1138 1045 HOH HOH . E 5 HOH A 39 1139 1005 HOH HOH . E 5 HOH A 40 1140 1003 HOH HOH . E 5 HOH A 41 1141 1062 HOH HOH . E 5 HOH A 42 1142 1009 HOH HOH . E 5 HOH A 43 1143 1054 HOH HOH . E 5 HOH A 44 1144 1022 HOH HOH . E 5 HOH A 45 1145 1013 HOH HOH . E 5 HOH A 46 1146 1116 HOH HOH . E 5 HOH A 47 1147 1038 HOH HOH . E 5 HOH A 48 1148 1007 HOH HOH . E 5 HOH A 49 1149 1036 HOH HOH . E 5 HOH A 50 1150 1107 HOH HOH . E 5 HOH A 51 1151 1104 HOH HOH . E 5 HOH A 52 1152 1041 HOH HOH . E 5 HOH A 53 1153 1056 HOH HOH . E 5 HOH A 54 1154 1020 HOH HOH . E 5 HOH A 55 1155 1114 HOH HOH . E 5 HOH A 56 1156 1006 HOH HOH . E 5 HOH A 57 1157 1079 HOH HOH . E 5 HOH A 58 1158 1083 HOH HOH . E 5 HOH A 59 1159 1034 HOH HOH . E 5 HOH A 60 1160 1102 HOH HOH . E 5 HOH A 61 1161 1008 HOH HOH . E 5 HOH A 62 1162 1091 HOH HOH . E 5 HOH A 63 1163 1030 HOH HOH . E 5 HOH A 64 1164 1002 HOH HOH . E 5 HOH A 65 1165 1052 HOH HOH . E 5 HOH A 66 1166 1103 HOH HOH . E 5 HOH A 67 1167 1090 HOH HOH . E 5 HOH A 68 1168 1059 HOH HOH . E 5 HOH A 69 1169 1014 HOH HOH . E 5 HOH A 70 1170 1040 HOH HOH . E 5 HOH A 71 1171 1053 HOH HOH . E 5 HOH A 72 1172 1112 HOH HOH . E 5 HOH A 73 1173 1037 HOH HOH . E 5 HOH A 74 1174 1004 HOH HOH . E 5 HOH A 75 1175 1067 HOH HOH . E 5 HOH A 76 1176 1017 HOH HOH . E 5 HOH A 77 1177 1028 HOH HOH . E 5 HOH A 78 1178 1043 HOH HOH . E 5 HOH A 79 1179 1035 HOH HOH . E 5 HOH A 80 1180 1042 HOH HOH . E 5 HOH A 81 1181 1031 HOH HOH . E 5 HOH A 82 1182 1075 HOH HOH . E 5 HOH A 83 1183 1060 HOH HOH . E 5 HOH A 84 1184 1078 HOH HOH . E 5 HOH A 85 1185 1088 HOH HOH . E 5 HOH A 86 1186 1099 HOH HOH . E 5 HOH A 87 1187 1019 HOH HOH . E 5 HOH A 88 1188 1087 HOH HOH . E 5 HOH A 89 1189 1039 HOH HOH . E 5 HOH A 90 1190 1016 HOH HOH . E 5 HOH A 91 1191 1024 HOH HOH . E 5 HOH A 92 1192 1058 HOH HOH . E 5 HOH A 93 1193 1068 HOH HOH . E 5 HOH A 94 1194 1074 HOH HOH . E 5 HOH A 95 1195 1011 HOH HOH . E 5 HOH A 96 1196 1098 HOH HOH . E 5 HOH A 97 1197 1084 HOH HOH . E 5 HOH A 98 1198 1085 HOH HOH . E 5 HOH A 99 1199 1057 HOH HOH . E 5 HOH A 100 1200 1025 HOH HOH . E 5 HOH A 101 1201 1018 HOH HOH . E 5 HOH A 102 1202 1063 HOH HOH . E 5 HOH A 103 1203 1064 HOH HOH . E 5 HOH A 104 1204 1077 HOH HOH . E 5 HOH A 105 1205 1021 HOH HOH . E 5 HOH A 106 1206 1108 HOH HOH . E 5 HOH A 107 1207 1117 HOH HOH . E 5 HOH A 108 1208 1093 HOH HOH . E 5 HOH A 109 1209 1029 HOH HOH . E 5 HOH A 110 1210 1073 HOH HOH . E 5 HOH A 111 1211 1071 HOH HOH . E 5 HOH A 112 1212 1086 HOH HOH . E 5 HOH A 113 1213 1094 HOH HOH . E 5 HOH A 114 1214 1097 HOH HOH . E 5 HOH A 115 1215 1115 HOH HOH . E 5 HOH A 116 1216 1118 HOH HOH . E 5 HOH A 117 1217 1120 HOH HOH . E 5 HOH A 118 1218 1105 HOH HOH . E 5 HOH A 119 1219 1092 HOH HOH . F 5 HOH B 1 401 373 HOH HOH . F 5 HOH B 2 402 414 HOH HOH . F 5 HOH B 3 403 436 HOH HOH . F 5 HOH B 4 404 413 HOH HOH . F 5 HOH B 5 405 372 HOH HOH . F 5 HOH B 6 406 426 HOH HOH . F 5 HOH B 7 407 324 HOH HOH . F 5 HOH B 8 408 405 HOH HOH . F 5 HOH B 9 409 417 HOH HOH . F 5 HOH B 10 410 357 HOH HOH . F 5 HOH B 11 411 316 HOH HOH . F 5 HOH B 12 412 346 HOH HOH . F 5 HOH B 13 413 334 HOH HOH . F 5 HOH B 14 414 396 HOH HOH . F 5 HOH B 15 415 364 HOH HOH . F 5 HOH B 16 416 439 HOH HOH . F 5 HOH B 17 417 337 HOH HOH . F 5 HOH B 18 418 356 HOH HOH . F 5 HOH B 19 419 420 HOH HOH . F 5 HOH B 20 420 320 HOH HOH . F 5 HOH B 21 421 348 HOH HOH . F 5 HOH B 22 422 393 HOH HOH . F 5 HOH B 23 423 395 HOH HOH . F 5 HOH B 24 424 323 HOH HOH . F 5 HOH B 25 425 381 HOH HOH . F 5 HOH B 26 426 302 HOH HOH . F 5 HOH B 27 427 387 HOH HOH . F 5 HOH B 28 428 308 HOH HOH . F 5 HOH B 29 429 397 HOH HOH . F 5 HOH B 30 430 338 HOH HOH . F 5 HOH B 31 431 288 HOH HOH . F 5 HOH B 32 432 345 HOH HOH . F 5 HOH B 33 433 350 HOH HOH . F 5 HOH B 34 434 394 HOH HOH . F 5 HOH B 35 435 347 HOH HOH . F 5 HOH B 36 436 313 HOH HOH . F 5 HOH B 37 437 298 HOH HOH . F 5 HOH B 38 438 423 HOH HOH . F 5 HOH B 39 439 412 HOH HOH . F 5 HOH B 40 440 293 HOH HOH . F 5 HOH B 41 441 309 HOH HOH . F 5 HOH B 42 442 307 HOH HOH . F 5 HOH B 43 443 295 HOH HOH . F 5 HOH B 44 444 365 HOH HOH . F 5 HOH B 45 445 314 HOH HOH . F 5 HOH B 46 446 327 HOH HOH . F 5 HOH B 47 447 433 HOH HOH . F 5 HOH B 48 448 363 HOH HOH . F 5 HOH B 49 449 336 HOH HOH . F 5 HOH B 50 450 391 HOH HOH . F 5 HOH B 51 451 341 HOH HOH . F 5 HOH B 52 452 430 HOH HOH . F 5 HOH B 53 453 303 HOH HOH . F 5 HOH B 54 454 322 HOH HOH . F 5 HOH B 55 455 330 HOH HOH . F 5 HOH B 56 456 289 HOH HOH . F 5 HOH B 57 457 331 HOH HOH . F 5 HOH B 58 458 312 HOH HOH . F 5 HOH B 59 459 318 HOH HOH . F 5 HOH B 60 460 399 HOH HOH . F 5 HOH B 61 461 305 HOH HOH . F 5 HOH B 62 462 353 HOH HOH . F 5 HOH B 63 463 306 HOH HOH . F 5 HOH B 64 464 375 HOH HOH . F 5 HOH B 65 465 291 HOH HOH . F 5 HOH B 66 466 377 HOH HOH . F 5 HOH B 67 467 429 HOH HOH . F 5 HOH B 68 468 432 HOH HOH . F 5 HOH B 69 469 294 HOH HOH . F 5 HOH B 70 470 301 HOH HOH . F 5 HOH B 71 471 407 HOH HOH . F 5 HOH B 72 472 292 HOH HOH . F 5 HOH B 73 473 408 HOH HOH . F 5 HOH B 74 474 359 HOH HOH . F 5 HOH B 75 475 300 HOH HOH . F 5 HOH B 76 476 388 HOH HOH . F 5 HOH B 77 477 384 HOH HOH . F 5 HOH B 78 478 342 HOH HOH . F 5 HOH B 79 479 299 HOH HOH . F 5 HOH B 80 480 339 HOH HOH . F 5 HOH B 81 481 424 HOH HOH . F 5 HOH B 82 482 315 HOH HOH . F 5 HOH B 83 483 317 HOH HOH . F 5 HOH B 84 484 360 HOH HOH . F 5 HOH B 85 485 335 HOH HOH . F 5 HOH B 86 486 437 HOH HOH . F 5 HOH B 87 487 403 HOH HOH . F 5 HOH B 88 488 386 HOH HOH . F 5 HOH B 89 489 379 HOH HOH . F 5 HOH B 90 490 326 HOH HOH . F 5 HOH B 91 491 371 HOH HOH . F 5 HOH B 92 492 319 HOH HOH . F 5 HOH B 93 493 361 HOH HOH . F 5 HOH B 94 494 367 HOH HOH . F 5 HOH B 95 495 296 HOH HOH . F 5 HOH B 96 496 290 HOH HOH . F 5 HOH B 97 497 355 HOH HOH . F 5 HOH B 98 498 333 HOH HOH . F 5 HOH B 99 499 401 HOH HOH . F 5 HOH B 100 500 427 HOH HOH . F 5 HOH B 101 501 344 HOH HOH . F 5 HOH B 102 502 415 HOH HOH . F 5 HOH B 103 503 385 HOH HOH . F 5 HOH B 104 504 421 HOH HOH . F 5 HOH B 105 505 389 HOH HOH . F 5 HOH B 106 506 398 HOH HOH . F 5 HOH B 107 507 422 HOH HOH . F 5 HOH B 108 508 351 HOH HOH . F 5 HOH B 109 509 418 HOH HOH . F 5 HOH B 110 510 311 HOH HOH . F 5 HOH B 111 511 400 HOH HOH . F 5 HOH B 112 512 383 HOH HOH . F 5 HOH B 113 513 343 HOH HOH . F 5 HOH B 114 514 352 HOH HOH . F 5 HOH B 115 515 362 HOH HOH . F 5 HOH B 116 516 332 HOH HOH . F 5 HOH B 117 517 425 HOH HOH . F 5 HOH B 118 518 340 HOH HOH . F 5 HOH B 119 519 369 HOH HOH . F 5 HOH B 120 520 428 HOH HOH . F 5 HOH B 121 521 354 HOH HOH . F 5 HOH B 122 522 304 HOH HOH . F 5 HOH B 123 523 419 HOH HOH . F 5 HOH B 124 524 310 HOH HOH . F 5 HOH B 125 525 325 HOH HOH . F 5 HOH B 126 526 406 HOH HOH . F 5 HOH B 127 527 380 HOH HOH . F 5 HOH B 128 528 390 HOH HOH . F 5 HOH B 129 529 349 HOH HOH . F 5 HOH B 130 530 402 HOH HOH . F 5 HOH B 131 531 416 HOH HOH . F 5 HOH B 132 532 404 HOH HOH . F 5 HOH B 133 533 374 HOH HOH . F 5 HOH B 134 534 328 HOH HOH . F 5 HOH B 135 535 409 HOH HOH . F 5 HOH B 136 536 366 HOH HOH . F 5 HOH B 137 537 382 HOH HOH . F 5 HOH B 138 538 410 HOH HOH . F 5 HOH B 139 539 329 HOH HOH . F 5 HOH B 140 540 411 HOH HOH . F 5 HOH B 141 541 378 HOH HOH . F 5 HOH B 142 542 297 HOH HOH . F 5 HOH B 143 543 370 HOH HOH . F 5 HOH B 144 544 358 HOH HOH . F 5 HOH B 145 545 368 HOH HOH . F 5 HOH B 146 546 376 HOH HOH . F 5 HOH B 147 547 435 HOH HOH . F 5 HOH B 148 548 434 HOH HOH . F 5 HOH B 149 549 287 HOH HOH . F 5 HOH B 150 550 321 HOH HOH . F 5 HOH B 151 551 431 HOH HOH . F 5 HOH B 152 552 392 HOH HOH . F 5 HOH B 153 553 438 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N GLY . . . C 3 10.012 99.206 404.034 1 25.18 ? N GLY 1001 A 1 HETATM 2 C CA GLY . . . C 3 9.593 98.37 405.154 1 22.66 ? CA GLY 1001 A 1 HETATM 3 C C GLY . . . C 3 9.29 96.935 404.764 1 25.78 ? C GLY 1001 A 1 HETATM 4 O O GLY . . . C 3 8.896 96.669 403.625 1 21.81 ? O GLY 1001 A 1 HETATM 5 O OXT GLY . . . C 3 9.451 95.999 405.56 1 20.25 ? OXT GLY 1001 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 5 #