data_4GVA # _model_server_result.job_id fLGbDYxtvFCL1fhbcwQtcQ _model_server_result.datetime_utc '2025-01-20 14:30:10' _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 4gva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4GVA # _exptl.entry_id 4GVA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 108.49 _cell.angle_gamma 90 _cell.entry_id 4GVA _cell.length_a 48.605 _cell.length_b 69.072 _cell.length_c 59.962 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GVA _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 covale ? covale1 A C THR 164 A THR 158 1_555 A N CME 165 A CME 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale2 A C CME 165 A CME 159 1_555 A N ASP 166 A ASP 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? # _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 4GVA _atom_sites.fract_transf_matrix[1][1] 0.020574 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006882 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014478 _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] 0.017585 _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 ADP A 1 401 1 ADP ADP . C 3 GOL A 1 402 1 GOL GOL . D 4 HOH A 1 501 1 HOH HOH . D 4 HOH A 2 502 2 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 5 HOH HOH . D 4 HOH A 6 506 6 HOH HOH . D 4 HOH A 7 507 7 HOH HOH . D 4 HOH A 8 508 8 HOH HOH . D 4 HOH A 9 509 9 HOH HOH . D 4 HOH A 10 510 10 HOH HOH . D 4 HOH A 11 511 11 HOH HOH . D 4 HOH A 12 512 12 HOH HOH . D 4 HOH A 13 513 13 HOH HOH . D 4 HOH A 14 514 14 HOH HOH . D 4 HOH A 15 515 15 HOH HOH . D 4 HOH A 16 516 16 HOH HOH . D 4 HOH A 17 517 17 HOH HOH . D 4 HOH A 18 518 18 HOH HOH . D 4 HOH A 19 519 19 HOH HOH . D 4 HOH A 20 520 20 HOH HOH . D 4 HOH A 21 521 21 HOH HOH . D 4 HOH A 22 522 22 HOH HOH . D 4 HOH A 23 523 23 HOH HOH . D 4 HOH A 24 524 24 HOH HOH . D 4 HOH A 25 525 25 HOH HOH . D 4 HOH A 26 526 26 HOH HOH . D 4 HOH A 27 527 27 HOH HOH . D 4 HOH A 28 528 28 HOH HOH . D 4 HOH A 29 529 29 HOH HOH . D 4 HOH A 30 530 30 HOH HOH . D 4 HOH A 31 531 31 HOH HOH . D 4 HOH A 32 532 32 HOH HOH . D 4 HOH A 33 533 33 HOH HOH . D 4 HOH A 34 534 34 HOH HOH . D 4 HOH A 35 535 35 HOH HOH . D 4 HOH A 36 536 36 HOH HOH . D 4 HOH A 37 537 37 HOH HOH . D 4 HOH A 38 538 38 HOH HOH . D 4 HOH A 39 539 39 HOH HOH . D 4 HOH A 40 540 40 HOH HOH . D 4 HOH A 41 541 41 HOH HOH . D 4 HOH A 42 542 42 HOH HOH . D 4 HOH A 43 543 43 HOH HOH . D 4 HOH A 44 544 44 HOH HOH . D 4 HOH A 45 545 45 HOH HOH . D 4 HOH A 46 546 46 HOH HOH . D 4 HOH A 47 547 47 HOH HOH . D 4 HOH A 48 548 48 HOH HOH . D 4 HOH A 49 549 49 HOH HOH . D 4 HOH A 50 550 50 HOH HOH . D 4 HOH A 51 551 51 HOH HOH . D 4 HOH A 52 552 52 HOH HOH . D 4 HOH A 53 553 53 HOH HOH . D 4 HOH A 54 554 54 HOH HOH . D 4 HOH A 55 555 55 HOH HOH . D 4 HOH A 56 556 56 HOH HOH . D 4 HOH A 57 557 57 HOH HOH . D 4 HOH A 58 558 58 HOH HOH . D 4 HOH A 59 559 59 HOH HOH . D 4 HOH A 60 560 60 HOH HOH . D 4 HOH A 61 561 61 HOH HOH . D 4 HOH A 62 562 62 HOH HOH . D 4 HOH A 63 563 63 HOH HOH . D 4 HOH A 64 564 64 HOH HOH . D 4 HOH A 65 565 65 HOH HOH . D 4 HOH A 66 566 66 HOH HOH . D 4 HOH A 67 567 67 HOH HOH . D 4 HOH A 68 568 68 HOH HOH . D 4 HOH A 69 569 69 HOH HOH . D 4 HOH A 70 570 70 HOH HOH . D 4 HOH A 71 571 71 HOH HOH . D 4 HOH A 72 572 72 HOH HOH . D 4 HOH A 73 573 73 HOH HOH . D 4 HOH A 74 574 74 HOH HOH . D 4 HOH A 75 575 75 HOH HOH . D 4 HOH A 76 576 76 HOH HOH . D 4 HOH A 77 577 77 HOH HOH . D 4 HOH A 78 578 78 HOH HOH . D 4 HOH A 79 579 80 HOH HOH . D 4 HOH A 80 580 81 HOH HOH . D 4 HOH A 81 581 82 HOH HOH . D 4 HOH A 82 582 83 HOH HOH . D 4 HOH A 83 583 84 HOH HOH . D 4 HOH A 84 584 85 HOH HOH . D 4 HOH A 85 585 86 HOH HOH . D 4 HOH A 86 586 87 HOH HOH . D 4 HOH A 87 587 88 HOH HOH . D 4 HOH A 88 588 89 HOH HOH . D 4 HOH A 89 589 92 HOH HOH . D 4 HOH A 90 590 93 HOH HOH . D 4 HOH A 91 591 94 HOH HOH . D 4 HOH A 92 592 95 HOH HOH . D 4 HOH A 93 593 98 HOH HOH . D 4 HOH A 94 594 100 HOH HOH . D 4 HOH A 95 595 101 HOH HOH . D 4 HOH A 96 596 102 HOH HOH . D 4 HOH A 97 597 103 HOH HOH . D 4 HOH A 98 598 104 HOH HOH . D 4 HOH A 99 599 105 HOH HOH . D 4 HOH A 100 600 106 HOH HOH . D 4 HOH A 101 601 107 HOH HOH . D 4 HOH A 102 602 108 HOH HOH . D 4 HOH A 103 603 109 HOH HOH . D 4 HOH A 104 604 110 HOH HOH . D 4 HOH A 105 605 112 HOH HOH . D 4 HOH A 106 606 113 HOH HOH . D 4 HOH A 107 607 114 HOH HOH . D 4 HOH A 108 608 116 HOH HOH . D 4 HOH A 109 609 117 HOH HOH . D 4 HOH A 110 610 118 HOH HOH . D 4 HOH A 111 611 119 HOH HOH . D 4 HOH A 112 612 120 HOH HOH . D 4 HOH A 113 613 121 HOH HOH . D 4 HOH A 114 614 122 HOH HOH . D 4 HOH A 115 615 123 HOH HOH . D 4 HOH A 116 616 124 HOH HOH . D 4 HOH A 117 617 125 HOH HOH . D 4 HOH A 118 618 127 HOH HOH . D 4 HOH A 119 619 128 HOH HOH . D 4 HOH A 120 620 129 HOH HOH . D 4 HOH A 121 621 130 HOH HOH . D 4 HOH A 122 622 131 HOH HOH . D 4 HOH A 123 623 132 HOH HOH . D 4 HOH A 124 624 134 HOH HOH . D 4 HOH A 125 625 135 HOH HOH . D 4 HOH A 126 626 136 HOH HOH . D 4 HOH A 127 627 138 HOH HOH . D 4 HOH A 128 628 140 HOH HOH . D 4 HOH A 129 629 141 HOH HOH . D 4 HOH A 130 630 142 HOH HOH . D 4 HOH A 131 631 143 HOH HOH . D 4 HOH A 132 632 144 HOH HOH . D 4 HOH A 133 633 147 HOH HOH . D 4 HOH A 134 634 148 HOH HOH . D 4 HOH A 135 635 149 HOH HOH . D 4 HOH A 136 636 150 HOH HOH . D 4 HOH A 137 637 151 HOH HOH . D 4 HOH A 138 638 152 HOH HOH . D 4 HOH A 139 639 153 HOH HOH . D 4 HOH A 140 640 154 HOH HOH . D 4 HOH A 141 641 155 HOH HOH . D 4 HOH A 142 642 156 HOH HOH . D 4 HOH A 143 643 157 HOH HOH . D 4 HOH A 144 644 158 HOH HOH . D 4 HOH A 145 645 159 HOH HOH . D 4 HOH A 146 646 160 HOH HOH . D 4 HOH A 147 647 161 HOH HOH . D 4 HOH A 148 648 162 HOH HOH . D 4 HOH A 149 649 163 HOH HOH . D 4 HOH A 150 650 164 HOH HOH . D 4 HOH A 151 651 165 HOH HOH . D 4 HOH A 152 652 166 HOH HOH . D 4 HOH A 153 653 167 HOH HOH . D 4 HOH A 154 654 169 HOH HOH . D 4 HOH A 155 655 170 HOH HOH . D 4 HOH A 156 656 171 HOH HOH . D 4 HOH A 157 657 172 HOH HOH . D 4 HOH A 158 658 173 HOH HOH . D 4 HOH A 159 659 174 HOH HOH . D 4 HOH A 160 660 175 HOH HOH . D 4 HOH A 161 661 176 HOH HOH . D 4 HOH A 162 662 177 HOH HOH . D 4 HOH A 163 663 178 HOH HOH . D 4 HOH A 164 664 179 HOH HOH . D 4 HOH A 165 665 180 HOH HOH . D 4 HOH A 166 666 181 HOH HOH . D 4 HOH A 167 667 182 HOH HOH . D 4 HOH A 168 668 183 HOH HOH . D 4 HOH A 169 669 184 HOH HOH . D 4 HOH A 170 670 185 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 . . . B 2 1.043 18.145 13.951 1 98.28 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -0.125 18.55 14.831 1 91.28 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 1.672 16.8 14.238 1 99.96 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 2.075 19.242 13.748 1 96.4 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -0.55 16.635 12.095 1 86.78 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -0.199 15.413 12.911 1 81.96 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -0.485 16.576 10.582 1 92.75 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 0.329 17.926 12.521 1 94.62 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -2.051 17.043 12.476 1 74.7 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -2.613 18.319 12.17 1 70.9 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -3.873 18.404 13.011 1 68.12 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -4.976 17.67 12.427 1 58.15 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -3.552 17.743 14.35 1 67.97 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -3.148 18.669 15.368 1 70.17 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -4.812 16.993 14.717 1 62.47 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -5.483 17.71 15.752 1 68.92 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -5.598 16.846 13.408 1 57.46 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -5.525 15.396 13.039 1 50.08 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -4.438 14.736 12.567 1 50.5 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -4.727 13.423 12.356 1 44.85 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6 13.203 12.69 1 42.11 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -6.92 12.039 12.709 1 40 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -6.533 10.787 12.304 1 39.41 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -8.181 12.25 13.121 1 43.96 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -8.633 13.473 13.519 1 44.67 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -7.862 14.57 13.54 1 46.23 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.537 14.509 13.147 1 48.77 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #