data_3VDI # _model_server_result.job_id vXCkrzAD4oq-uEX1GLxmIQ _model_server_result.datetime_utc '2024-12-18 10:44:06' _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 3vdi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":409}' # _entry.id 3VDI # _exptl.entry_id 3VDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 194.226 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'TETRAETHYLENE GLYCOL' _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 3VDI _cell.length_a 83.967 _cell.length_b 83.967 _cell.length_c 115.724 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _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[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -41.9835 72.717555 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -83.967 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N 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 metalc ? metalc1 A O LEU 243 A LEU 238 1_555 F MG BCL . A BCL 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc2 C MG BCL . A BCL 402 1_555 M O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? # _chem_comp.formula 'C8 H18 O5' _chem_comp.formula_weight 194.226 _chem_comp.id PG4 _chem_comp.mon_nstd_flag . _chem_comp.name 'TETRAETHYLENE GLYCOL' _chem_comp.type non-polymer _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 O1 C1 PG4 sing 385 n n O1 HO1 PG4 sing 386 n n C1 C2 PG4 sing 387 n n C1 H11 PG4 sing 388 n n C1 H12 PG4 sing 389 n n C2 O2 PG4 sing 390 n n C2 H21 PG4 sing 391 n n C2 H22 PG4 sing 392 n n O2 C3 PG4 sing 393 n n C3 C4 PG4 sing 394 n n C3 H31 PG4 sing 395 n n C3 H32 PG4 sing 396 n n C4 O3 PG4 sing 397 n n C4 H41 PG4 sing 398 n n C4 H42 PG4 sing 399 n n O3 C5 PG4 sing 400 n n C5 C6 PG4 sing 401 n n C5 H51 PG4 sing 402 n n C5 H52 PG4 sing 403 n n C6 O4 PG4 sing 404 n n C6 H61 PG4 sing 405 n n C6 H62 PG4 sing 406 n n O4 C7 PG4 sing 407 n n C7 C8 PG4 sing 408 n n C7 H71 PG4 sing 409 n n C7 H72 PG4 sing 410 n n C8 O5 PG4 sing 411 n n C8 H81 PG4 sing 412 n n C8 H82 PG4 sing 413 n n O5 HO5 PG4 sing 414 n n # _atom_sites.entry_id 3VDI _atom_sites.fract_transf_matrix[1][1] 0.011909 _atom_sites.fract_transf_matrix[1][2] 0.006876 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013752 _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] 0.008641 _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 B 2 BCL A 1 401 401 BCL BCL . C 2 BCL A 1 402 402 BCL BCL . D 2 BCL A 1 403 403 BCL BCL . E 2 BCL A 1 404 404 BCL BCL . F 2 BCL A 1 405 405 BCL BCL . G 2 BCL A 1 406 406 BCL BCL . H 2 BCL A 1 407 407 BCL BCL . I 3 PG4 A 1 408 408 PG4 PG4 . J 3 PG4 A 1 409 2001 PG4 PG4 . K 3 PG4 A 1 410 2002 PG4 PG4 . L 3 PG4 A 1 411 2003 PG4 PG4 . M 4 HOH A 1 1001 1001 HOH HOH . M 4 HOH A 2 1002 1002 HOH HOH . M 4 HOH A 3 1003 364 HOH HOH . M 4 HOH A 4 1004 365 HOH HOH . M 4 HOH A 5 1005 366 HOH HOH . M 4 HOH A 6 1006 367 HOH HOH . M 4 HOH A 7 1007 368 HOH HOH . M 4 HOH A 8 1008 369 HOH HOH . M 4 HOH A 9 1009 370 HOH HOH . M 4 HOH A 10 1010 371 HOH HOH . M 4 HOH A 11 1011 372 HOH HOH . M 4 HOH A 12 1012 373 HOH HOH . M 4 HOH A 13 1013 374 HOH HOH . M 4 HOH A 14 1014 375 HOH HOH . M 4 HOH A 15 1015 376 HOH HOH . M 4 HOH A 16 1016 377 HOH HOH . M 4 HOH A 17 1017 378 HOH HOH . M 4 HOH A 18 1018 379 HOH HOH . M 4 HOH A 19 1019 380 HOH HOH . M 4 HOH A 20 1020 381 HOH HOH . M 4 HOH A 21 1021 382 HOH HOH . M 4 HOH A 22 1022 383 HOH HOH . M 4 HOH A 23 1023 384 HOH HOH . M 4 HOH A 24 1024 385 HOH HOH . M 4 HOH A 25 1025 386 HOH HOH . M 4 HOH A 26 1026 387 HOH HOH . M 4 HOH A 27 1027 388 HOH HOH . M 4 HOH A 28 1028 389 HOH HOH . M 4 HOH A 29 1029 390 HOH HOH . M 4 HOH A 30 1030 391 HOH HOH . M 4 HOH A 31 1031 393 HOH HOH . M 4 HOH A 32 1032 394 HOH HOH . M 4 HOH A 33 1033 396 HOH HOH . M 4 HOH A 34 1034 397 HOH HOH . M 4 HOH A 35 1035 399 HOH HOH . M 4 HOH A 36 1036 409 HOH HOH . M 4 HOH A 37 1037 410 HOH HOH . M 4 HOH A 38 1038 411 HOH HOH . M 4 HOH A 39 1039 412 HOH HOH . M 4 HOH A 40 1040 413 HOH HOH . M 4 HOH A 41 1041 414 HOH HOH . M 4 HOH A 42 1042 415 HOH HOH . M 4 HOH A 43 1043 416 HOH HOH . M 4 HOH A 44 1044 417 HOH HOH . M 4 HOH A 45 1045 418 HOH HOH . M 4 HOH A 46 1046 419 HOH HOH . M 4 HOH A 47 1047 420 HOH HOH . M 4 HOH A 48 1048 421 HOH HOH . M 4 HOH A 49 1049 423 HOH HOH . M 4 HOH A 50 1050 424 HOH HOH . M 4 HOH A 51 1051 426 HOH HOH . M 4 HOH A 52 1052 427 HOH HOH . M 4 HOH A 53 1053 428 HOH HOH . M 4 HOH A 54 1054 429 HOH HOH . M 4 HOH A 55 1055 430 HOH HOH . M 4 HOH A 56 1056 431 HOH HOH . M 4 HOH A 57 1057 432 HOH HOH . M 4 HOH A 58 1058 433 HOH HOH . M 4 HOH A 59 1059 434 HOH HOH . M 4 HOH A 60 1060 436 HOH HOH . M 4 HOH A 61 1061 437 HOH HOH . M 4 HOH A 62 1062 438 HOH HOH . M 4 HOH A 63 1063 439 HOH HOH . M 4 HOH A 64 1064 443 HOH HOH . M 4 HOH A 65 1065 445 HOH HOH . M 4 HOH A 66 1066 446 HOH HOH . M 4 HOH A 67 1067 447 HOH HOH . M 4 HOH A 68 1068 448 HOH HOH . M 4 HOH A 69 1069 450 HOH HOH . M 4 HOH A 70 1070 451 HOH HOH . M 4 HOH A 71 1071 452 HOH HOH . M 4 HOH A 72 1072 453 HOH HOH . M 4 HOH A 73 1073 455 HOH HOH . M 4 HOH A 74 1074 456 HOH HOH . M 4 HOH A 75 1075 457 HOH HOH . M 4 HOH A 76 1076 458 HOH HOH . M 4 HOH A 77 1077 459 HOH HOH . M 4 HOH A 78 1078 461 HOH HOH . M 4 HOH A 79 1079 462 HOH HOH . M 4 HOH A 80 1080 463 HOH HOH . M 4 HOH A 81 1081 464 HOH HOH . M 4 HOH A 82 1082 465 HOH HOH . M 4 HOH A 83 1083 466 HOH HOH . M 4 HOH A 84 1084 468 HOH HOH . M 4 HOH A 85 1085 469 HOH HOH . M 4 HOH A 86 1086 470 HOH HOH . M 4 HOH A 87 1087 472 HOH HOH . M 4 HOH A 88 1088 473 HOH HOH . M 4 HOH A 89 1089 475 HOH HOH . M 4 HOH A 90 1090 478 HOH HOH . M 4 HOH A 91 1091 479 HOH HOH . M 4 HOH A 92 1092 480 HOH HOH . M 4 HOH A 93 1093 483 HOH HOH . M 4 HOH A 94 1094 484 HOH HOH . M 4 HOH A 95 1095 486 HOH HOH . M 4 HOH A 96 1096 487 HOH HOH . M 4 HOH A 97 1097 488 HOH HOH . M 4 HOH A 98 1098 489 HOH HOH . M 4 HOH A 99 1099 491 HOH HOH . M 4 HOH A 100 1100 492 HOH HOH . M 4 HOH A 101 1101 496 HOH HOH . M 4 HOH A 102 1102 497 HOH HOH . M 4 HOH A 103 1103 498 HOH HOH . M 4 HOH A 104 1104 499 HOH HOH . M 4 HOH A 105 1105 501 HOH HOH . M 4 HOH A 106 1106 503 HOH HOH . M 4 HOH A 107 1107 504 HOH HOH . M 4 HOH A 108 1108 507 HOH HOH . M 4 HOH A 109 1109 508 HOH HOH . M 4 HOH A 110 1110 510 HOH HOH . M 4 HOH A 111 1111 511 HOH HOH . M 4 HOH A 112 1112 512 HOH HOH . M 4 HOH A 113 1113 515 HOH HOH . M 4 HOH A 114 1114 516 HOH HOH . M 4 HOH A 115 1115 517 HOH HOH . M 4 HOH A 116 1116 518 HOH HOH . M 4 HOH A 117 1117 519 HOH HOH . M 4 HOH A 118 1118 521 HOH HOH . M 4 HOH A 119 1119 522 HOH HOH . M 4 HOH A 120 1120 524 HOH HOH . M 4 HOH A 121 1121 526 HOH HOH . M 4 HOH A 122 1122 528 HOH HOH . M 4 HOH A 123 1123 533 HOH HOH . M 4 HOH A 124 1124 535 HOH HOH . M 4 HOH A 125 1125 536 HOH HOH . M 4 HOH A 126 1126 537 HOH HOH . M 4 HOH A 127 1127 541 HOH HOH . M 4 HOH A 128 1128 542 HOH HOH . M 4 HOH A 129 1129 545 HOH HOH . M 4 HOH A 130 1130 546 HOH HOH . M 4 HOH A 131 1131 548 HOH HOH . M 4 HOH A 132 1132 549 HOH HOH . M 4 HOH A 133 1133 551 HOH HOH . M 4 HOH A 134 1134 552 HOH HOH . M 4 HOH A 135 1135 553 HOH HOH . M 4 HOH A 136 1136 554 HOH HOH . M 4 HOH A 137 1137 555 HOH HOH . M 4 HOH A 138 1138 557 HOH HOH . M 4 HOH A 139 1139 558 HOH HOH . M 4 HOH A 140 1140 560 HOH HOH . M 4 HOH A 141 1141 561 HOH HOH . M 4 HOH A 142 1142 562 HOH HOH . M 4 HOH A 143 1143 563 HOH HOH . M 4 HOH A 144 1144 565 HOH HOH . M 4 HOH A 145 1145 567 HOH HOH . M 4 HOH A 146 1146 568 HOH HOH . M 4 HOH A 147 1147 570 HOH HOH . M 4 HOH A 148 1148 571 HOH HOH . M 4 HOH A 149 1149 573 HOH HOH . M 4 HOH A 150 1150 574 HOH HOH . M 4 HOH A 151 1151 577 HOH HOH . M 4 HOH A 152 1152 580 HOH HOH . M 4 HOH A 153 1153 582 HOH HOH . M 4 HOH A 154 1154 583 HOH HOH . M 4 HOH A 155 1155 584 HOH HOH . M 4 HOH A 156 1156 585 HOH HOH . M 4 HOH A 157 1157 587 HOH HOH . M 4 HOH A 158 1158 589 HOH HOH . M 4 HOH A 159 1159 594 HOH HOH . M 4 HOH A 160 1160 598 HOH HOH . M 4 HOH A 161 1161 599 HOH HOH . M 4 HOH A 162 1162 603 HOH HOH . M 4 HOH A 163 1163 604 HOH HOH . M 4 HOH A 164 1164 607 HOH HOH . M 4 HOH A 165 1165 608 HOH HOH . M 4 HOH A 166 1166 610 HOH HOH . M 4 HOH A 167 1167 612 HOH HOH . M 4 HOH A 168 1168 613 HOH HOH . M 4 HOH A 169 1169 618 HOH HOH . M 4 HOH A 170 1170 619 HOH HOH . M 4 HOH A 171 1171 622 HOH HOH . M 4 HOH A 172 1172 626 HOH HOH . M 4 HOH A 173 1173 628 HOH HOH . M 4 HOH A 174 1174 629 HOH HOH . M 4 HOH A 175 1175 631 HOH HOH . M 4 HOH A 176 1176 632 HOH HOH . M 4 HOH A 177 1177 633 HOH HOH . M 4 HOH A 178 1178 637 HOH HOH . M 4 HOH A 179 1179 639 HOH HOH . M 4 HOH A 180 1180 643 HOH HOH . M 4 HOH A 181 1181 646 HOH HOH . M 4 HOH A 182 1182 655 HOH HOH . M 4 HOH A 183 1183 656 HOH HOH . M 4 HOH A 184 1184 658 HOH HOH . M 4 HOH A 185 1185 671 HOH HOH . M 4 HOH A 186 1186 676 HOH HOH . M 4 HOH A 187 1187 681 HOH HOH . M 4 HOH A 188 1188 683 HOH HOH . M 4 HOH A 189 1189 685 HOH HOH . M 4 HOH A 190 1190 686 HOH HOH . M 4 HOH A 191 1191 687 HOH HOH . M 4 HOH A 192 1192 693 HOH HOH . M 4 HOH A 193 1193 694 HOH HOH . M 4 HOH A 194 1194 696 HOH HOH . M 4 HOH A 195 1195 703 HOH HOH . M 4 HOH A 196 1196 705 HOH HOH . M 4 HOH A 197 1197 707 HOH HOH . M 4 HOH A 198 1198 711 HOH HOH . M 4 HOH A 199 1199 713 HOH HOH . M 4 HOH A 200 1200 714 HOH HOH . M 4 HOH A 201 1201 715 HOH HOH . M 4 HOH A 202 1202 717 HOH HOH . M 4 HOH A 203 1203 718 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 O O2 PG4 . . . J 3 -34.218 48.962 5.249 0.99 42.19 ? O2 PG4 409 A 1 HETATM 2 C C3 PG4 . . . J 3 -35.238 48.369 6.089 0.99 41.49 ? C3 PG4 409 A 1 HETATM 3 C C4 PG4 . . . J 3 -34.686 47.308 7.041 0.99 40.72 ? C4 PG4 409 A 1 HETATM 4 O O3 PG4 . . . J 3 -34.099 46.258 6.296 0.99 40.54 ? O3 PG4 409 A 1 HETATM 5 C C5 PG4 . . . J 3 -33.983 45.095 7.084 0.99 39.77 ? C5 PG4 409 A 1 HETATM 6 C C6 PG4 . . . J 3 -33.162 44.064 6.307 0.99 39.7 ? C6 PG4 409 A 1 HETATM 7 O O4 PG4 . . . J 3 -33.896 43.711 5.174 0.99 39.79 ? O4 PG4 409 A 1 HETATM 8 C C7 PG4 . . . J 3 -33.196 42.745 4.358 0.99 39.74 ? C7 PG4 409 A 1 HETATM 9 C C8 PG4 . . . J 3 -33.876 42.706 2.972 0.99 40.17 ? C8 PG4 409 A 1 HETATM 10 O O5 PG4 . . . J 3 -34.199 41.366 2.597 0.99 39.78 ? O5 PG4 409 A 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #