data_8VME # _model_server_result.job_id TjcZoyA1AyapS4eHN1QCgg _model_server_result.datetime_utc '2024-11-01 19:34:33' _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 8vme # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":405}' # _entry.id 8VME # _exptl.entry_id 8VME _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 6 _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 8VME _cell.length_a 82.257 _cell.length_b 82.257 _cell.length_c 280.99 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VME _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _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,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 H N N ? 6 I N N ? 6 J N N ? 6 K N N ? 6 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 covale ? covale1 C C PRO 11 C PRO 44 1_555 C N SEP 12 C SEP 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 C C SEP 12 C SEP 45 1_555 C N LEU 13 C LEU 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD1 ASN 162 A ASN 186 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc2 A OD2 ASP 176 A ASP 200 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc3 A OD1 ASP 176 A ASP 200 1_555 F MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc4 A OD2 ASP 176 A ASP 200 1_555 F MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc5 D O1B ADP . A ADP 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc6 D O1A ADP . A ADP 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc7 D O3B ADP . A ADP 401 1_555 F MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc8 F MG MG . A MG 403 1_555 N O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc9 F MG MG . A MG 403 1_555 N O HOH . A HOH 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc10 F MG MG . A MG 403 1_555 N O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc11 M NA NA . A NA 410 1_555 N O HOH . A HOH 646 8_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 173 n n C1 C2 GOL sing 174 n n C1 H11 GOL sing 175 n n C1 H12 GOL sing 176 n n O1 HO1 GOL sing 177 n n C2 O2 GOL sing 178 n n C2 C3 GOL sing 179 n n C2 H2 GOL sing 180 n n O2 HO2 GOL sing 181 n n C3 O3 GOL sing 182 n n C3 H31 GOL sing 183 n n C3 H32 GOL sing 184 n n O3 HO3 GOL sing 185 n n # _atom_sites.entry_id 8VME _atom_sites.fract_transf_matrix[1][1] 0.012157 _atom_sites.fract_transf_matrix[1][2] 0.007019 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014038 _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] 0.003559 _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 D 4 ADP A 1 401 1 ADP ADP . E 5 MG A 1 402 1 MG MG . F 5 MG A 1 403 3 MG MG . G 6 GOL A 1 404 1 GOL GOL . H 6 GOL A 1 405 2 GOL GOL . I 6 GOL A 1 406 5 GOL GOL . J 6 GOL A 1 407 7 GOL GOL . K 6 GOL A 1 408 8 GOL GOL . L 6 GOL A 1 409 9 GOL GOL . M 7 NA A 1 410 1 NA NA . N 8 HOH A 1 501 386 HOH HOH . N 8 HOH A 2 502 358 HOH HOH . N 8 HOH A 3 503 394 HOH HOH . N 8 HOH A 4 504 381 HOH HOH . N 8 HOH A 5 505 390 HOH HOH . N 8 HOH A 6 506 372 HOH HOH . N 8 HOH A 7 507 401 HOH HOH . N 8 HOH A 8 508 397 HOH HOH . N 8 HOH A 9 509 342 HOH HOH . N 8 HOH A 10 510 346 HOH HOH . N 8 HOH A 11 511 209 HOH HOH . N 8 HOH A 12 512 39 HOH HOH . N 8 HOH A 13 513 364 HOH HOH . N 8 HOH A 14 514 340 HOH HOH . N 8 HOH A 15 515 7 HOH HOH . N 8 HOH A 16 516 370 HOH HOH . N 8 HOH A 17 517 30 HOH HOH . N 8 HOH A 18 518 1 HOH HOH . N 8 HOH A 19 519 101 HOH HOH . N 8 HOH A 20 520 389 HOH HOH . N 8 HOH A 21 521 88 HOH HOH . N 8 HOH A 22 522 87 HOH HOH . N 8 HOH A 23 523 22 HOH HOH . N 8 HOH A 24 524 74 HOH HOH . N 8 HOH A 25 525 19 HOH HOH . N 8 HOH A 26 526 374 HOH HOH . N 8 HOH A 27 527 145 HOH HOH . N 8 HOH A 28 528 338 HOH HOH . N 8 HOH A 29 529 5 HOH HOH . N 8 HOH A 30 530 33 HOH HOH . N 8 HOH A 31 531 55 HOH HOH . N 8 HOH A 32 532 360 HOH HOH . N 8 HOH A 33 533 367 HOH HOH . N 8 HOH A 34 534 35 HOH HOH . N 8 HOH A 35 535 57 HOH HOH . N 8 HOH A 36 536 49 HOH HOH . N 8 HOH A 37 537 335 HOH HOH . N 8 HOH A 38 538 46 HOH HOH . N 8 HOH A 39 539 6 HOH HOH . N 8 HOH A 40 540 44 HOH HOH . N 8 HOH A 41 541 334 HOH HOH . N 8 HOH A 42 542 43 HOH HOH . N 8 HOH A 43 543 113 HOH HOH . N 8 HOH A 44 544 120 HOH HOH . N 8 HOH A 45 545 32 HOH HOH . N 8 HOH A 46 546 333 HOH HOH . N 8 HOH A 47 547 28 HOH HOH . N 8 HOH A 48 548 317 HOH HOH . N 8 HOH A 49 549 50 HOH HOH . N 8 HOH A 50 550 93 HOH HOH . N 8 HOH A 51 551 196 HOH HOH . N 8 HOH A 52 552 4 HOH HOH . N 8 HOH A 53 553 363 HOH HOH . N 8 HOH A 54 554 322 HOH HOH . N 8 HOH A 55 555 3 HOH HOH . N 8 HOH A 56 556 10 HOH HOH . N 8 HOH A 57 557 76 HOH HOH . N 8 HOH A 58 558 48 HOH HOH . N 8 HOH A 59 559 382 HOH HOH . N 8 HOH A 60 560 75 HOH HOH . N 8 HOH A 61 561 9 HOH HOH . N 8 HOH A 62 562 350 HOH HOH . N 8 HOH A 63 563 132 HOH HOH . N 8 HOH A 64 564 51 HOH HOH . N 8 HOH A 65 565 41 HOH HOH . N 8 HOH A 66 566 352 HOH HOH . N 8 HOH A 67 567 343 HOH HOH . N 8 HOH A 68 568 328 HOH HOH . N 8 HOH A 69 569 8 HOH HOH . N 8 HOH A 70 570 18 HOH HOH . N 8 HOH A 71 571 82 HOH HOH . N 8 HOH A 72 572 73 HOH HOH . N 8 HOH A 73 573 223 HOH HOH . N 8 HOH A 74 574 34 HOH HOH . N 8 HOH A 75 575 20 HOH HOH . N 8 HOH A 76 576 354 HOH HOH . N 8 HOH A 77 577 347 HOH HOH . N 8 HOH A 78 578 387 HOH HOH . N 8 HOH A 79 579 13 HOH HOH . N 8 HOH A 80 580 385 HOH HOH . N 8 HOH A 81 581 47 HOH HOH . N 8 HOH A 82 582 318 HOH HOH . N 8 HOH A 83 583 40 HOH HOH . N 8 HOH A 84 584 348 HOH HOH . N 8 HOH A 85 585 324 HOH HOH . N 8 HOH A 86 586 365 HOH HOH . N 8 HOH A 87 587 186 HOH HOH . N 8 HOH A 88 588 42 HOH HOH . N 8 HOH A 89 589 24 HOH HOH . N 8 HOH A 90 590 265 HOH HOH . N 8 HOH A 91 591 349 HOH HOH . N 8 HOH A 92 592 279 HOH HOH . N 8 HOH A 93 593 59 HOH HOH . N 8 HOH A 94 594 158 HOH HOH . N 8 HOH A 95 595 353 HOH HOH . N 8 HOH A 96 596 214 HOH HOH . N 8 HOH A 97 597 141 HOH HOH . N 8 HOH A 98 598 69 HOH HOH . N 8 HOH A 99 599 379 HOH HOH . N 8 HOH A 100 600 108 HOH HOH . N 8 HOH A 101 601 14 HOH HOH . N 8 HOH A 102 602 375 HOH HOH . N 8 HOH A 103 603 337 HOH HOH . N 8 HOH A 104 604 351 HOH HOH . N 8 HOH A 105 605 359 HOH HOH . N 8 HOH A 106 606 90 HOH HOH . N 8 HOH A 107 607 54 HOH HOH . N 8 HOH A 108 608 344 HOH HOH . N 8 HOH A 109 609 83 HOH HOH . N 8 HOH A 110 610 16 HOH HOH . N 8 HOH A 111 611 384 HOH HOH . N 8 HOH A 112 612 65 HOH HOH . N 8 HOH A 113 613 287 HOH HOH . N 8 HOH A 114 614 80 HOH HOH . N 8 HOH A 115 615 99 HOH HOH . N 8 HOH A 116 616 128 HOH HOH . N 8 HOH A 117 617 66 HOH HOH . N 8 HOH A 118 618 140 HOH HOH . N 8 HOH A 119 619 153 HOH HOH . N 8 HOH A 120 620 37 HOH HOH . N 8 HOH A 121 621 345 HOH HOH . N 8 HOH A 122 622 131 HOH HOH . N 8 HOH A 123 623 91 HOH HOH . N 8 HOH A 124 624 15 HOH HOH . N 8 HOH A 125 625 200 HOH HOH . N 8 HOH A 126 626 62 HOH HOH . N 8 HOH A 127 627 391 HOH HOH . N 8 HOH A 128 628 151 HOH HOH . N 8 HOH A 129 629 84 HOH HOH . N 8 HOH A 130 630 17 HOH HOH . N 8 HOH A 131 631 21 HOH HOH . N 8 HOH A 132 632 378 HOH HOH . N 8 HOH A 133 633 400 HOH HOH . N 8 HOH A 134 634 260 HOH HOH . N 8 HOH A 135 635 98 HOH HOH . N 8 HOH A 136 636 170 HOH HOH . N 8 HOH A 137 637 185 HOH HOH . N 8 HOH A 138 638 392 HOH HOH . N 8 HOH A 139 639 119 HOH HOH . N 8 HOH A 140 640 321 HOH HOH . N 8 HOH A 141 641 63 HOH HOH . N 8 HOH A 142 642 104 HOH HOH . N 8 HOH A 143 643 388 HOH HOH . N 8 HOH A 144 644 199 HOH HOH . N 8 HOH A 145 645 377 HOH HOH . N 8 HOH A 146 646 361 HOH HOH . N 8 HOH A 147 647 112 HOH HOH . N 8 HOH A 148 648 395 HOH HOH . N 8 HOH A 149 649 371 HOH HOH . N 8 HOH A 150 650 393 HOH HOH . N 8 HOH A 151 651 399 HOH HOH . N 8 HOH A 152 652 380 HOH HOH . N 8 HOH A 153 653 58 HOH HOH . N 8 HOH A 154 654 100 HOH HOH . N 8 HOH A 155 655 164 HOH HOH . N 8 HOH A 156 656 67 HOH HOH . N 8 HOH A 157 657 130 HOH HOH . N 8 HOH A 158 658 326 HOH HOH . N 8 HOH A 159 659 383 HOH HOH . N 8 HOH A 160 660 147 HOH HOH . N 8 HOH A 161 661 187 HOH HOH . N 8 HOH A 162 662 310 HOH HOH . N 8 HOH A 163 663 356 HOH HOH . N 8 HOH A 164 664 160 HOH HOH . N 8 HOH A 165 665 92 HOH HOH . O 8 HOH B 1 501 323 HOH HOH . O 8 HOH B 2 502 332 HOH HOH . O 8 HOH B 3 503 339 HOH HOH . O 8 HOH B 4 504 64 HOH HOH . O 8 HOH B 5 505 52 HOH HOH . O 8 HOH B 6 506 121 HOH HOH . O 8 HOH B 7 507 23 HOH HOH . O 8 HOH B 8 508 25 HOH HOH . O 8 HOH B 9 509 396 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 C C1 GOL . . . H 6 12.91 -23.972 -2.413 1 107.09 ? C1 GOL 405 A 1 HETATM 2 O O1 GOL . . . H 6 14.288 -23.942 -2.088 1 96.13 ? O1 GOL 405 A 1 HETATM 3 C C2 GOL . . . H 6 12.449 -22.802 -3.38 1 116.84 ? C2 GOL 405 A 1 HETATM 4 O O2 GOL . . . H 6 12.93 -21.521 -3.029 1 126.64 ? O2 GOL 405 A 1 HETATM 5 C C3 GOL . . . H 6 12.867 -23.156 -4.862 1 87.67 ? C3 GOL 405 A 1 HETATM 6 O O3 GOL . . . H 6 13.244 -21.93 -5.566 1 87.94 ? O3 GOL 405 A 1 HETATM 7 H H11 GOL . . . H 6 12.671 -24.809 -2.841 1 128.5 ? H11 GOL 405 A 1 HETATM 8 H H12 GOL . . . H 6 12.362 -23.917 -1.614 1 128.5 ? H12 GOL 405 A 1 HETATM 9 H HO1 GOL . . . H 6 14.698 -24.235 -2.781 1 115.35 ? HO1 GOL 405 A 1 HETATM 10 H H2 GOL . . . H 6 11.483 -22.774 -3.295 1 140.21 ? H2 GOL 405 A 1 HETATM 11 H HO2 GOL . . . H 6 13.323 -21.184 -3.719 1 151.97 ? HO2 GOL 405 A 1 HETATM 12 H H31 GOL . . . H 6 13.586 -23.806 -4.825 1 105.21 ? H31 GOL 405 A 1 HETATM 13 H H32 GOL . . . H 6 12.125 -23.619 -5.282 1 105.21 ? H32 GOL 405 A 1 HETATM 14 H HO3 GOL . . . H 6 12.555 -21.611 -5.942 1 105.52 ? HO3 GOL 405 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 14 #