data_1VJD # _model_server_result.job_id ljetDSzkalcFr6wVlGSjiw _model_server_result.datetime_utc '2024-11-07 05:33:07' _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 1vjd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":417}' # _entry.id 1VJD # _exptl.entry_id 1VJD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 97.8 _cell.angle_gamma 90 _cell.entry_id 1VJD _cell.length_a 36.2 _cell.length_b 106.4 _cell.length_c 51.1 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VJD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 1VJD _atom_sites.fract_transf_matrix[1][1] 0.027624 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003784 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009398 _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] 0.019752 _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 PO4 A 1 418 418 PO4 PO4 . C 3 ATP A 1 417 417 ATP ATP . D 4 HOH A 1 419 419 HOH TIP . D 4 HOH A 2 424 424 HOH TIP . D 4 HOH A 3 425 425 HOH TIP . D 4 HOH A 4 426 426 HOH TIP . D 4 HOH A 5 427 427 HOH TIP . D 4 HOH A 6 428 428 HOH TIP . D 4 HOH A 7 429 429 HOH TIP . D 4 HOH A 8 430 430 HOH TIP . D 4 HOH A 9 431 431 HOH TIP . D 4 HOH A 10 432 432 HOH TIP . D 4 HOH A 11 433 433 HOH TIP . D 4 HOH A 12 434 434 HOH TIP . D 4 HOH A 13 435 435 HOH TIP . D 4 HOH A 14 436 436 HOH TIP . D 4 HOH A 15 437 437 HOH TIP . D 4 HOH A 16 438 438 HOH TIP . D 4 HOH A 17 439 439 HOH TIP . D 4 HOH A 18 440 440 HOH TIP . D 4 HOH A 19 441 441 HOH TIP . D 4 HOH A 20 442 442 HOH TIP . D 4 HOH A 21 443 443 HOH TIP . D 4 HOH A 22 444 444 HOH TIP . D 4 HOH A 23 445 445 HOH TIP . D 4 HOH A 24 446 446 HOH TIP . D 4 HOH A 25 447 447 HOH TIP . D 4 HOH A 26 448 448 HOH TIP . D 4 HOH A 27 449 449 HOH TIP . D 4 HOH A 28 450 450 HOH TIP . D 4 HOH A 29 451 451 HOH TIP . D 4 HOH A 30 452 452 HOH TIP . D 4 HOH A 31 453 453 HOH TIP . D 4 HOH A 32 454 454 HOH TIP . D 4 HOH A 33 455 455 HOH TIP . D 4 HOH A 34 456 456 HOH TIP . D 4 HOH A 35 457 457 HOH TIP . D 4 HOH A 36 458 458 HOH TIP . D 4 HOH A 37 459 459 HOH TIP . D 4 HOH A 38 460 460 HOH TIP . D 4 HOH A 39 461 461 HOH TIP . D 4 HOH A 40 462 462 HOH TIP . D 4 HOH A 41 463 463 HOH TIP . D 4 HOH A 42 464 464 HOH TIP . D 4 HOH A 43 465 465 HOH TIP . D 4 HOH A 44 466 466 HOH TIP . D 4 HOH A 45 467 467 HOH TIP . D 4 HOH A 46 468 468 HOH TIP . D 4 HOH A 47 469 469 HOH TIP . D 4 HOH A 48 470 470 HOH TIP . D 4 HOH A 49 471 471 HOH TIP . D 4 HOH A 50 472 472 HOH TIP . D 4 HOH A 51 473 473 HOH TIP . D 4 HOH A 52 474 474 HOH TIP . D 4 HOH A 53 475 475 HOH TIP . D 4 HOH A 54 476 476 HOH TIP . D 4 HOH A 55 477 477 HOH TIP . D 4 HOH A 56 478 478 HOH TIP . D 4 HOH A 57 479 479 HOH TIP . D 4 HOH A 58 480 480 HOH TIP . D 4 HOH A 59 481 481 HOH TIP . D 4 HOH A 60 482 482 HOH TIP . D 4 HOH A 61 483 483 HOH TIP . D 4 HOH A 62 484 484 HOH TIP . D 4 HOH A 63 485 485 HOH TIP . D 4 HOH A 64 486 486 HOH TIP . D 4 HOH A 65 487 487 HOH TIP . D 4 HOH A 66 488 488 HOH TIP . D 4 HOH A 67 491 491 HOH TIP . D 4 HOH A 68 492 492 HOH TIP . D 4 HOH A 69 493 493 HOH TIP . D 4 HOH A 70 494 494 HOH TIP . D 4 HOH A 71 495 495 HOH TIP . D 4 HOH A 72 496 496 HOH TIP . D 4 HOH A 73 497 497 HOH TIP . D 4 HOH A 74 498 498 HOH TIP . D 4 HOH A 75 499 499 HOH TIP . D 4 HOH A 76 500 500 HOH TIP . D 4 HOH A 77 501 501 HOH TIP . D 4 HOH A 78 502 502 HOH TIP . D 4 HOH A 79 503 503 HOH TIP . D 4 HOH A 80 504 504 HOH TIP . D 4 HOH A 81 505 505 HOH TIP . D 4 HOH A 82 506 506 HOH TIP . D 4 HOH A 83 507 507 HOH TIP . D 4 HOH A 84 508 508 HOH TIP . D 4 HOH A 85 510 510 HOH TIP . D 4 HOH A 86 511 511 HOH TIP . D 4 HOH A 87 512 512 HOH TIP . D 4 HOH A 88 513 513 HOH TIP . D 4 HOH A 89 514 514 HOH TIP . D 4 HOH A 90 515 515 HOH TIP . D 4 HOH A 91 516 516 HOH TIP . D 4 HOH A 92 517 517 HOH TIP . D 4 HOH A 93 518 518 HOH TIP . D 4 HOH A 94 519 519 HOH TIP . D 4 HOH A 95 520 520 HOH TIP . D 4 HOH A 96 521 521 HOH TIP . D 4 HOH A 97 522 522 HOH TIP . D 4 HOH A 98 523 523 HOH TIP . D 4 HOH A 99 524 524 HOH TIP . D 4 HOH A 100 525 525 HOH TIP . D 4 HOH A 101 526 526 HOH TIP . D 4 HOH A 102 527 527 HOH TIP . D 4 HOH A 103 528 528 HOH TIP . D 4 HOH A 104 529 529 HOH TIP . D 4 HOH A 105 530 530 HOH TIP . D 4 HOH A 106 531 531 HOH TIP . D 4 HOH A 107 532 532 HOH TIP . D 4 HOH A 108 533 533 HOH TIP . D 4 HOH A 109 534 534 HOH TIP . D 4 HOH A 110 535 535 HOH TIP . D 4 HOH A 111 536 536 HOH TIP . D 4 HOH A 112 537 537 HOH TIP . D 4 HOH A 113 539 539 HOH TIP . D 4 HOH A 114 541 541 HOH TIP . D 4 HOH A 115 542 542 HOH TIP . D 4 HOH A 116 543 543 HOH TIP . D 4 HOH A 117 544 544 HOH TIP . D 4 HOH A 118 545 545 HOH TIP . D 4 HOH A 119 546 546 HOH TIP . D 4 HOH A 120 547 547 HOH TIP . D 4 HOH A 121 549 549 HOH TIP . D 4 HOH A 122 550 550 HOH TIP . D 4 HOH A 123 551 551 HOH TIP . D 4 HOH A 124 552 552 HOH TIP . D 4 HOH A 125 553 553 HOH TIP . D 4 HOH A 126 554 554 HOH TIP . D 4 HOH A 127 555 555 HOH TIP . D 4 HOH A 128 556 556 HOH TIP . D 4 HOH A 129 557 557 HOH TIP . D 4 HOH A 130 558 558 HOH TIP . D 4 HOH A 131 559 559 HOH TIP . D 4 HOH A 132 560 560 HOH TIP . D 4 HOH A 133 561 561 HOH TIP . D 4 HOH A 134 563 563 HOH TIP . D 4 HOH A 135 564 564 HOH TIP . D 4 HOH A 136 565 565 HOH TIP . D 4 HOH A 137 566 566 HOH TIP . D 4 HOH A 138 568 568 HOH TIP . D 4 HOH A 139 569 569 HOH TIP . D 4 HOH A 140 570 570 HOH TIP . D 4 HOH A 141 571 571 HOH TIP . D 4 HOH A 142 572 572 HOH TIP . D 4 HOH A 143 573 573 HOH TIP . D 4 HOH A 144 574 574 HOH TIP . D 4 HOH A 145 575 575 HOH TIP . D 4 HOH A 146 576 576 HOH TIP . D 4 HOH A 147 577 577 HOH TIP . D 4 HOH A 148 578 578 HOH TIP . D 4 HOH A 149 579 579 HOH TIP . D 4 HOH A 150 580 580 HOH TIP . D 4 HOH A 151 581 581 HOH TIP . D 4 HOH A 152 582 582 HOH TIP . D 4 HOH A 153 583 583 HOH TIP . D 4 HOH A 154 584 584 HOH TIP . D 4 HOH A 155 585 585 HOH TIP . D 4 HOH A 156 586 586 HOH TIP . D 4 HOH A 157 588 588 HOH TIP . D 4 HOH A 158 589 589 HOH TIP . # 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 P PG ATP . . . C 3 7.283 4.183 7.401 1 65.47 ? PG ATP 417 A 1 HETATM 2 O O1G ATP . . . C 3 8.339 4.684 6.498 1 62.64 ? O1G ATP 417 A 1 HETATM 3 O O2G ATP . . . C 3 7.364 2.746 7.712 1 63.37 ? O2G ATP 417 A 1 HETATM 4 O O3G ATP . . . C 3 7.021 5.098 8.566 1 63.34 ? O3G ATP 417 A 1 HETATM 5 P PB ATP . . . C 3 5.613 4.956 5.064 1 63.64 ? PB ATP 417 A 1 HETATM 6 O O1B ATP . . . C 3 6.801 5.798 4.704 1 63.06 ? O1B ATP 417 A 1 HETATM 7 O O2B ATP . . . C 3 4.295 5.61 5.144 1 61.91 ? O2B ATP 417 A 1 HETATM 8 O O3B ATP . . . C 3 5.942 4.206 6.496 1 63.2 ? O3B ATP 417 A 1 HETATM 9 P PA ATP . . . C 3 5.232 3.447 2.572 1 58.98 ? PA ATP 417 A 1 HETATM 10 O O1A ATP . . . C 3 5.437 2.014 2.328 1 59.23 ? O1A ATP 417 A 1 HETATM 11 O O2A ATP . . . C 3 3.918 4.05 2.216 1 58.87 ? O2A ATP 417 A 1 HETATM 12 O O3A ATP . . . C 3 5.643 3.744 4.082 1 59.98 ? O3A ATP 417 A 1 HETATM 13 O O5' ATP . . . C 3 6.369 4.224 1.83 1 55.98 ? O5' ATP 417 A 1 HETATM 14 C C5' ATP . . . C 3 7.758 4.105 2.167 1 49.58 ? C5' ATP 417 A 1 HETATM 15 C C4' ATP . . . C 3 8.546 3.937 0.905 1 44.86 ? C4' ATP 417 A 1 HETATM 16 O O4' ATP . . . C 3 8.346 5.136 0.128 1 38.28 ? O4' ATP 417 A 1 HETATM 17 C C3' ATP . . . C 3 10.037 3.837 1.096 1 42.22 ? C3' ATP 417 A 1 HETATM 18 O O3' ATP . . . C 3 10.468 2.494 0.826 1 40.35 ? O3' ATP 417 A 1 HETATM 19 C C2' ATP . . . C 3 10.61 4.849 0.12 1 38.81 ? C2' ATP 417 A 1 HETATM 20 O O2' ATP . . . C 3 11.616 4.322 -0.724 1 38.63 ? O2' ATP 417 A 1 HETATM 21 C C1' ATP . . . C 3 9.417 5.224 -0.79 1 36.41 ? C1' ATP 417 A 1 HETATM 22 N N9 ATP . . . C 3 9.483 6.613 -1.341 1 28.54 ? N9 ATP 417 A 1 HETATM 23 C C8 ATP . . . C 3 9.688 7.804 -0.682 1 26.14 ? C8 ATP 417 A 1 HETATM 24 N N7 ATP . . . C 3 9.697 8.862 -1.442 1 25 ? N7 ATP 417 A 1 HETATM 25 C C5 ATP . . . C 3 9.483 8.327 -2.706 1 25.74 ? C5 ATP 417 A 1 HETATM 26 C C6 ATP . . . C 3 9.377 8.915 -3.999 1 19.88 ? C6 ATP 417 A 1 HETATM 27 N N6 ATP . . . C 3 9.493 10.225 -4.167 1 23.41 ? N6 ATP 417 A 1 HETATM 28 N N1 ATP . . . C 3 9.155 8.11 -5.075 1 23.54 ? N1 ATP 417 A 1 HETATM 29 C C2 ATP . . . C 3 9.04 6.787 -4.898 1 20.21 ? C2 ATP 417 A 1 HETATM 30 N N3 ATP . . . C 3 9.12 6.101 -3.733 1 24.41 ? N3 ATP 417 A 1 HETATM 31 C C4 ATP . . . C 3 9.344 6.953 -2.658 1 26.61 ? C4 ATP 417 A 1 # _model_server_stats.io_time_ms 94 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #