data_1VFZ # _model_server_result.job_id ECjmbJwUzw5FSoMcnmDx1A _model_server_result.datetime_utc '2025-07-06 10:57:41' _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 1vfz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1VFZ # _exptl.entry_id 1VFZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 1VFZ _cell.length_a 41.471 _cell.length_b 51.805 _cell.length_c 156.992 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VFZ _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 ? _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,E _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 4 _struct_asym.id D _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 metalc ? metalc1 A OG SER 104 A SER 104 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc2 D O3B ADP . A ADP 500 1_555 C MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc3 C MG MG . A MG 501 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc4 C MG MG . A MG 501 1_555 E O HOH . A HOH 594 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc5 C MG MG . A MG 501 1_555 E O HOH . A HOH 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc6 C MG MG . A MG 501 1_555 E O HOH . A HOH 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1VFZ _atom_sites.fract_transf_matrix[1][1] 0.024113 _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] 0.019303 _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] 0.00637 _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 VO4 A 1 400 400 VO4 VO4 . C 3 MG A 1 501 501 MG MG . D 4 ADP A 1 500 500 ADP ADP . E 5 HOH A 1 502 502 HOH HOH . E 5 HOH A 2 503 503 HOH HOH . E 5 HOH A 3 504 504 HOH HOH . E 5 HOH A 4 505 505 HOH HOH . E 5 HOH A 5 506 506 HOH HOH . E 5 HOH A 6 507 507 HOH HOH . E 5 HOH A 7 508 508 HOH HOH . E 5 HOH A 8 509 509 HOH HOH . E 5 HOH A 9 510 510 HOH HOH . E 5 HOH A 10 511 511 HOH HOH . E 5 HOH A 11 512 512 HOH HOH . E 5 HOH A 12 513 513 HOH HOH . E 5 HOH A 13 514 514 HOH HOH . E 5 HOH A 14 515 515 HOH HOH . E 5 HOH A 15 516 516 HOH HOH . E 5 HOH A 16 517 517 HOH HOH . E 5 HOH A 17 518 518 HOH HOH . E 5 HOH A 18 519 519 HOH HOH . E 5 HOH A 19 520 520 HOH HOH . E 5 HOH A 20 521 521 HOH HOH . E 5 HOH A 21 522 522 HOH HOH . E 5 HOH A 22 523 523 HOH HOH . E 5 HOH A 23 524 524 HOH HOH . E 5 HOH A 24 525 525 HOH HOH . E 5 HOH A 25 526 526 HOH HOH . E 5 HOH A 26 527 527 HOH HOH . E 5 HOH A 27 528 528 HOH HOH . E 5 HOH A 28 529 529 HOH HOH . E 5 HOH A 29 530 530 HOH HOH . E 5 HOH A 30 531 531 HOH HOH . E 5 HOH A 31 532 532 HOH HOH . E 5 HOH A 32 533 533 HOH HOH . E 5 HOH A 33 534 534 HOH HOH . E 5 HOH A 34 535 535 HOH HOH . E 5 HOH A 35 536 536 HOH HOH . E 5 HOH A 36 537 537 HOH HOH . E 5 HOH A 37 538 538 HOH HOH . E 5 HOH A 38 539 539 HOH HOH . E 5 HOH A 39 540 540 HOH HOH . E 5 HOH A 40 541 541 HOH HOH . E 5 HOH A 41 542 542 HOH HOH . E 5 HOH A 42 543 543 HOH HOH . E 5 HOH A 43 544 544 HOH HOH . E 5 HOH A 44 545 545 HOH HOH . E 5 HOH A 45 546 546 HOH HOH . E 5 HOH A 46 547 547 HOH HOH . E 5 HOH A 47 548 548 HOH HOH . E 5 HOH A 48 549 549 HOH HOH . E 5 HOH A 49 550 550 HOH HOH . E 5 HOH A 50 551 551 HOH HOH . E 5 HOH A 51 552 552 HOH HOH . E 5 HOH A 52 553 553 HOH HOH . E 5 HOH A 53 554 554 HOH HOH . E 5 HOH A 54 555 555 HOH HOH . E 5 HOH A 55 556 556 HOH HOH . E 5 HOH A 56 557 557 HOH HOH . E 5 HOH A 57 558 558 HOH HOH . E 5 HOH A 58 559 559 HOH HOH . E 5 HOH A 59 560 560 HOH HOH . E 5 HOH A 60 561 561 HOH HOH . E 5 HOH A 61 562 562 HOH HOH . E 5 HOH A 62 563 563 HOH HOH . E 5 HOH A 63 564 564 HOH HOH . E 5 HOH A 64 565 565 HOH HOH . E 5 HOH A 65 566 566 HOH HOH . E 5 HOH A 66 567 567 HOH HOH . E 5 HOH A 67 568 568 HOH HOH . E 5 HOH A 68 569 569 HOH HOH . E 5 HOH A 69 570 570 HOH HOH . E 5 HOH A 70 571 571 HOH HOH . E 5 HOH A 71 572 572 HOH HOH . E 5 HOH A 72 573 573 HOH HOH . E 5 HOH A 73 574 574 HOH HOH . E 5 HOH A 74 575 575 HOH HOH . E 5 HOH A 75 576 576 HOH HOH . E 5 HOH A 76 577 577 HOH HOH . E 5 HOH A 77 578 578 HOH HOH . E 5 HOH A 78 579 579 HOH HOH . E 5 HOH A 79 580 580 HOH HOH . E 5 HOH A 80 581 581 HOH HOH . E 5 HOH A 81 582 582 HOH HOH . E 5 HOH A 82 583 583 HOH HOH . E 5 HOH A 83 584 584 HOH HOH . E 5 HOH A 84 585 585 HOH HOH . E 5 HOH A 85 586 586 HOH HOH . E 5 HOH A 86 587 587 HOH HOH . E 5 HOH A 87 588 588 HOH HOH . E 5 HOH A 88 589 589 HOH HOH . E 5 HOH A 89 590 590 HOH HOH . E 5 HOH A 90 591 591 HOH HOH . E 5 HOH A 91 592 592 HOH HOH . E 5 HOH A 92 593 593 HOH HOH . E 5 HOH A 93 594 594 HOH HOH . E 5 HOH A 94 595 595 HOH HOH . E 5 HOH A 95 596 596 HOH HOH . E 5 HOH A 96 597 597 HOH HOH . E 5 HOH A 97 598 598 HOH HOH . E 5 HOH A 98 599 599 HOH HOH . E 5 HOH A 99 600 600 HOH HOH . E 5 HOH A 100 601 601 HOH HOH . E 5 HOH A 101 602 602 HOH HOH . E 5 HOH A 102 603 603 HOH HOH . E 5 HOH A 103 604 604 HOH HOH . E 5 HOH A 104 605 605 HOH HOH . E 5 HOH A 105 606 606 HOH HOH . E 5 HOH A 106 607 607 HOH HOH . E 5 HOH A 107 608 608 HOH HOH . E 5 HOH A 108 609 609 HOH HOH . E 5 HOH A 109 610 610 HOH HOH . E 5 HOH A 110 611 611 HOH HOH . E 5 HOH A 111 612 612 HOH HOH . E 5 HOH A 112 613 613 HOH HOH . E 5 HOH A 113 614 614 HOH HOH . E 5 HOH A 114 615 615 HOH HOH . E 5 HOH A 115 616 616 HOH HOH . E 5 HOH A 116 617 617 HOH HOH . E 5 HOH A 117 618 618 HOH HOH . E 5 HOH A 118 619 619 HOH HOH . E 5 HOH A 119 620 620 HOH HOH . E 5 HOH A 120 621 621 HOH HOH . E 5 HOH A 121 622 622 HOH HOH . E 5 HOH A 122 623 623 HOH HOH . E 5 HOH A 123 624 624 HOH HOH . E 5 HOH A 124 625 625 HOH HOH . E 5 HOH A 125 626 626 HOH HOH . E 5 HOH A 126 627 627 HOH HOH . E 5 HOH A 127 628 628 HOH HOH . E 5 HOH A 128 629 629 HOH HOH . E 5 HOH A 129 630 630 HOH HOH . E 5 HOH A 130 631 631 HOH HOH . E 5 HOH A 131 632 632 HOH HOH . E 5 HOH A 132 633 633 HOH HOH . E 5 HOH A 133 634 634 HOH HOH . E 5 HOH A 134 635 635 HOH HOH . E 5 HOH A 135 636 636 HOH HOH . E 5 HOH A 136 637 637 HOH HOH . E 5 HOH A 137 638 638 HOH HOH . E 5 HOH A 138 639 639 HOH HOH . E 5 HOH A 139 640 640 HOH HOH . E 5 HOH A 140 641 641 HOH HOH . E 5 HOH A 141 642 642 HOH HOH . E 5 HOH A 142 643 643 HOH HOH . E 5 HOH A 143 644 644 HOH HOH . E 5 HOH A 144 645 645 HOH HOH . E 5 HOH A 145 646 646 HOH HOH . E 5 HOH A 146 647 647 HOH HOH . E 5 HOH A 147 648 648 HOH HOH . E 5 HOH A 148 649 649 HOH HOH . E 5 HOH A 149 650 650 HOH HOH . E 5 HOH A 150 651 651 HOH HOH . E 5 HOH A 151 652 652 HOH HOH . E 5 HOH A 152 653 653 HOH HOH . E 5 HOH A 153 654 654 HOH HOH . E 5 HOH A 154 655 655 HOH HOH . E 5 HOH A 155 656 656 HOH HOH . E 5 HOH A 156 657 657 HOH HOH . E 5 HOH A 157 658 658 HOH HOH . E 5 HOH A 158 659 659 HOH HOH . E 5 HOH A 159 660 660 HOH HOH . E 5 HOH A 160 661 661 HOH HOH . E 5 HOH A 161 662 662 HOH HOH . E 5 HOH A 162 663 663 HOH HOH . E 5 HOH A 163 664 664 HOH HOH . E 5 HOH A 164 665 665 HOH HOH . E 5 HOH A 165 666 666 HOH HOH . E 5 HOH A 166 667 667 HOH HOH . E 5 HOH A 167 668 668 HOH HOH . E 5 HOH A 168 669 669 HOH HOH . E 5 HOH A 169 670 670 HOH HOH . E 5 HOH A 170 671 671 HOH HOH . E 5 HOH A 171 672 672 HOH HOH . E 5 HOH A 172 673 673 HOH HOH . E 5 HOH A 173 674 674 HOH HOH . E 5 HOH A 174 675 675 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 P PB ADP . . . D 4 24.058 -19.551 7.173 1 16.84 ? PB ADP 500 A 1 HETATM 2 O O1B ADP . . . D 4 25.381 -19.959 6.604 1 21.24 ? O1B ADP 500 A 1 HETATM 3 O O2B ADP . . . D 4 22.813 -20.164 6.499 1 32.26 ? O2B ADP 500 A 1 HETATM 4 O O3B ADP . . . D 4 23.988 -19.694 8.678 1 19.02 ? O3B ADP 500 A 1 HETATM 5 P PA ADP . . . D 4 22.692 -16.875 6.729 1 25.35 ? PA ADP 500 A 1 HETATM 6 O O1A ADP . . . D 4 21.97 -17.629 7.79 1 29.87 ? O1A ADP 500 A 1 HETATM 7 O O2A ADP . . . D 4 23.905 -16.067 6.737 1 27.91 ? O2A ADP 500 A 1 HETATM 8 O O3A ADP . . . D 4 23.884 -17.993 6.95 1 28.02 ? O3A ADP 500 A 1 HETATM 9 O O5' ADP . . . D 4 22.371 -17.493 5.301 1 31.95 ? O5' ADP 500 A 1 HETATM 10 C C5' ADP . . . D 4 23.012 -16.893 4.152 1 35.38 ? C5' ADP 500 A 1 HETATM 11 C C4' ADP . . . D 4 22.375 -15.674 3.487 1 27.98 ? C4' ADP 500 A 1 HETATM 12 O O4' ADP . . . D 4 21.062 -15.977 2.934 1 26.96 ? O4' ADP 500 A 1 HETATM 13 C C3' ADP . . . D 4 22.183 -14.339 4.247 1 34.75 ? C3' ADP 500 A 1 HETATM 14 O O3' ADP . . . D 4 22.734 -13.264 3.451 1 21.54 ? O3' ADP 500 A 1 HETATM 15 C C2' ADP . . . D 4 20.617 -14.095 4.318 1 29.34 ? C2' ADP 500 A 1 HETATM 16 O O2' ADP . . . D 4 20.234 -12.732 4.017 1 47.42 ? O2' ADP 500 A 1 HETATM 17 C C1' ADP . . . D 4 20.007 -15.066 3.27 1 24.09 ? C1' ADP 500 A 1 HETATM 18 N N9 ADP . . . D 4 18.745 -15.782 3.738 1 23.07 ? N9 ADP 500 A 1 HETATM 19 C C8 ADP . . . D 4 18.623 -17.021 4.197 1 32.88 ? C8 ADP 500 A 1 HETATM 20 N N7 ADP . . . D 4 17.416 -17.314 4.555 1 38.09 ? N7 ADP 500 A 1 HETATM 21 C C5 ADP . . . D 4 16.701 -16.133 4.371 1 25.03 ? C5 ADP 500 A 1 HETATM 22 C C6 ADP . . . D 4 15.293 -15.736 4.534 1 28.21 ? C6 ADP 500 A 1 HETATM 23 N N6 ADP . . . D 4 14.321 -16.568 5.02 1 27.37 ? N6 ADP 500 A 1 HETATM 24 N N1 ADP . . . D 4 14.956 -14.443 4.224 1 32.04 ? N1 ADP 500 A 1 HETATM 25 C C2 ADP . . . D 4 15.884 -13.598 3.767 1 27.66 ? C2 ADP 500 A 1 HETATM 26 N N3 ADP . . . D 4 17.187 -13.883 3.553 1 31.21 ? N3 ADP 500 A 1 HETATM 27 C C4 ADP . . . D 4 17.546 -15.157 3.914 1 24.25 ? C4 ADP 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #