data_5J9A # _model_server_result.job_id 3wmnC488bPPetk9hyGE4fw _model_server_result.datetime_utc '2024-11-25 13:24:35' _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 5j9a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 5J9A # _exptl.entry_id 5J9A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 5J9A _cell.length_a 66.038 _cell.length_b 72.047 _cell.length_c 80.237 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J9A _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 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,E,F _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 5 _struct_asym.id E _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 B O1 NO3 . A NO3 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc2 C MG MG . A MG 402 1_555 E O1B ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc3 C MG MG . A MG 402 1_555 E O1A ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc4 C MG MG . A MG 402 1_555 F O HOH . A HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc5 C MG MG . A MG 402 1_555 F O HOH . A HOH 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc6 C MG MG . A MG 402 1_555 F O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? # _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 5J9A _atom_sites.fract_transf_matrix[1][1] 0.015143 _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] 0.01388 _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] 0.012463 _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 NO3 A 1 401 405 NO3 NO3 . C 3 MG A 1 402 408 MG MG . D 4 ARG A 1 403 403 ARG ARG . E 5 ADP A 1 404 400 ADP ADP . F 6 HOH A 1 501 145 HOH HOH . F 6 HOH A 2 502 113 HOH HOH . F 6 HOH A 3 503 92 HOH HOH . F 6 HOH A 4 504 107 HOH HOH . F 6 HOH A 5 505 86 HOH HOH . F 6 HOH A 6 506 39 HOH HOH . F 6 HOH A 7 507 90 HOH HOH . F 6 HOH A 8 508 74 HOH HOH . F 6 HOH A 9 509 5 HOH HOH . F 6 HOH A 10 510 41 HOH HOH . F 6 HOH A 11 511 140 HOH HOH . F 6 HOH A 12 512 51 HOH HOH . F 6 HOH A 13 513 50 HOH HOH . F 6 HOH A 14 514 105 HOH HOH . F 6 HOH A 15 515 34 HOH HOH . F 6 HOH A 16 516 139 HOH HOH . F 6 HOH A 17 517 114 HOH HOH . F 6 HOH A 18 518 146 HOH HOH . F 6 HOH A 19 519 27 HOH HOH . F 6 HOH A 20 520 75 HOH HOH . F 6 HOH A 21 521 35 HOH HOH . F 6 HOH A 22 522 59 HOH HOH . F 6 HOH A 23 523 87 HOH HOH . F 6 HOH A 24 524 95 HOH HOH . F 6 HOH A 25 525 149 HOH HOH . F 6 HOH A 26 526 99 HOH HOH . F 6 HOH A 27 527 4 HOH HOH . F 6 HOH A 28 528 80 HOH HOH . F 6 HOH A 29 529 15 HOH HOH . F 6 HOH A 30 530 81 HOH HOH . F 6 HOH A 31 531 43 HOH HOH . F 6 HOH A 32 532 31 HOH HOH . F 6 HOH A 33 533 21 HOH HOH . F 6 HOH A 34 534 112 HOH HOH . F 6 HOH A 35 535 66 HOH HOH . F 6 HOH A 36 536 131 HOH HOH . F 6 HOH A 37 537 147 HOH HOH . F 6 HOH A 38 538 28 HOH HOH . F 6 HOH A 39 539 1 HOH HOH . F 6 HOH A 40 540 54 HOH HOH . F 6 HOH A 41 541 37 HOH HOH . F 6 HOH A 42 542 136 HOH HOH . F 6 HOH A 43 543 118 HOH HOH . F 6 HOH A 44 544 47 HOH HOH . F 6 HOH A 45 545 2 HOH HOH . F 6 HOH A 46 546 103 HOH HOH . F 6 HOH A 47 547 68 HOH HOH . F 6 HOH A 48 548 61 HOH HOH . F 6 HOH A 49 549 58 HOH HOH . F 6 HOH A 50 550 18 HOH HOH . F 6 HOH A 51 551 141 HOH HOH . F 6 HOH A 52 552 19 HOH HOH . F 6 HOH A 53 553 26 HOH HOH . F 6 HOH A 54 554 60 HOH HOH . F 6 HOH A 55 555 69 HOH HOH . F 6 HOH A 56 556 42 HOH HOH . F 6 HOH A 57 557 7 HOH HOH . F 6 HOH A 58 558 65 HOH HOH . F 6 HOH A 59 559 67 HOH HOH . F 6 HOH A 60 560 71 HOH HOH . F 6 HOH A 61 561 49 HOH HOH . F 6 HOH A 62 562 22 HOH HOH . F 6 HOH A 63 563 79 HOH HOH . F 6 HOH A 64 564 150 HOH HOH . F 6 HOH A 65 565 97 HOH HOH . F 6 HOH A 66 566 76 HOH HOH . F 6 HOH A 67 567 88 HOH HOH . F 6 HOH A 68 568 127 HOH HOH . F 6 HOH A 69 569 33 HOH HOH . F 6 HOH A 70 570 56 HOH HOH . F 6 HOH A 71 571 3 HOH HOH . F 6 HOH A 72 572 78 HOH HOH . F 6 HOH A 73 573 6 HOH HOH . F 6 HOH A 74 574 72 HOH HOH . F 6 HOH A 75 575 143 HOH HOH . F 6 HOH A 76 576 40 HOH HOH . F 6 HOH A 77 577 83 HOH HOH . F 6 HOH A 78 578 117 HOH HOH . F 6 HOH A 79 579 106 HOH HOH . F 6 HOH A 80 580 64 HOH HOH . F 6 HOH A 81 581 20 HOH HOH . F 6 HOH A 82 582 8 HOH HOH . F 6 HOH A 83 583 77 HOH HOH . F 6 HOH A 84 584 10 HOH HOH . F 6 HOH A 85 585 13 HOH HOH . F 6 HOH A 86 586 44 HOH HOH . F 6 HOH A 87 587 9 HOH HOH . F 6 HOH A 88 588 115 HOH HOH . F 6 HOH A 89 589 29 HOH HOH . F 6 HOH A 90 590 25 HOH HOH . F 6 HOH A 91 591 132 HOH HOH . F 6 HOH A 92 592 98 HOH HOH . F 6 HOH A 93 593 30 HOH HOH . F 6 HOH A 94 594 129 HOH HOH . F 6 HOH A 95 595 93 HOH HOH . F 6 HOH A 96 596 11 HOH HOH . F 6 HOH A 97 597 82 HOH HOH . F 6 HOH A 98 598 12 HOH HOH . F 6 HOH A 99 599 73 HOH HOH . F 6 HOH A 100 600 32 HOH HOH . F 6 HOH A 101 601 45 HOH HOH . F 6 HOH A 102 602 24 HOH HOH . F 6 HOH A 103 603 17 HOH HOH . F 6 HOH A 104 604 142 HOH HOH . F 6 HOH A 105 605 89 HOH HOH . F 6 HOH A 106 606 91 HOH HOH . F 6 HOH A 107 607 101 HOH HOH . F 6 HOH A 108 608 144 HOH HOH . F 6 HOH A 109 609 53 HOH HOH . F 6 HOH A 110 610 16 HOH HOH . F 6 HOH A 111 611 134 HOH HOH . F 6 HOH A 112 612 109 HOH HOH . F 6 HOH A 113 613 128 HOH HOH . F 6 HOH A 114 614 62 HOH HOH . F 6 HOH A 115 615 133 HOH HOH . F 6 HOH A 116 616 138 HOH HOH . F 6 HOH A 117 617 57 HOH HOH . F 6 HOH A 118 618 70 HOH HOH . F 6 HOH A 119 619 14 HOH HOH . F 6 HOH A 120 620 48 HOH HOH . F 6 HOH A 121 621 121 HOH HOH . F 6 HOH A 122 622 104 HOH HOH . F 6 HOH A 123 623 46 HOH HOH . F 6 HOH A 124 624 36 HOH HOH . F 6 HOH A 125 625 100 HOH HOH . F 6 HOH A 126 626 122 HOH HOH . F 6 HOH A 127 627 116 HOH HOH . F 6 HOH A 128 628 137 HOH HOH . F 6 HOH A 129 629 119 HOH HOH . F 6 HOH A 130 630 126 HOH HOH . F 6 HOH A 131 631 94 HOH HOH . F 6 HOH A 132 632 23 HOH HOH . F 6 HOH A 133 633 148 HOH HOH . F 6 HOH A 134 634 52 HOH HOH . F 6 HOH A 135 635 125 HOH HOH . F 6 HOH A 136 636 111 HOH HOH . F 6 HOH A 137 637 85 HOH HOH . F 6 HOH A 138 638 151 HOH HOH . F 6 HOH A 139 639 123 HOH HOH . F 6 HOH A 140 640 102 HOH HOH . F 6 HOH A 141 641 124 HOH HOH . F 6 HOH A 142 642 135 HOH HOH . F 6 HOH A 143 643 55 HOH HOH . F 6 HOH A 144 644 38 HOH HOH . F 6 HOH A 145 645 108 HOH HOH . F 6 HOH A 146 646 96 HOH HOH . F 6 HOH A 147 647 84 HOH HOH . F 6 HOH A 148 648 130 HOH HOH . F 6 HOH A 149 649 63 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 . . . E 5 22.859 10.73 38.62 1 24.57 ? PB ADP 404 A 1 HETATM 2 O O1B ADP . . . E 5 23.805 10.543 37.478 1 24.89 ? O1B ADP 404 A 1 HETATM 3 O O2B ADP . . . E 5 21.555 11.156 38.02 1 34.35 ? O2B ADP 404 A 1 HETATM 4 O O3B ADP . . . E 5 22.708 9.594 39.516 1 31.72 ? O3B ADP 404 A 1 HETATM 5 P PA ADP . . . E 5 24.581 12.91 39.858 1 25.75 ? PA ADP 404 A 1 HETATM 6 O O1A ADP . . . E 5 25.514 12.583 38.743 1 23.93 ? O1A ADP 404 A 1 HETATM 7 O O2A ADP . . . E 5 24.9 12.842 41.289 1 22.8 ? O2A ADP 404 A 1 HETATM 8 O O3A ADP . . . E 5 23.314 11.903 39.689 1 23.11 ? O3A ADP 404 A 1 HETATM 9 O O5' ADP . . . E 5 23.826 14.309 39.576 1 28.38 ? O5' ADP 404 A 1 HETATM 10 C C5' ADP . . . E 5 23.399 14.598 38.238 1 27.33 ? C5' ADP 404 A 1 HETATM 11 C C4' ADP . . . E 5 22.612 15.909 38.239 1 25.84 ? C4' ADP 404 A 1 HETATM 12 O O4' ADP . . . E 5 21.359 15.692 38.871 1 23.04 ? O4' ADP 404 A 1 HETATM 13 C C3' ADP . . . E 5 23.319 17.019 38.988 1 28.15 ? C3' ADP 404 A 1 HETATM 14 O O3' ADP . . . E 5 23.077 18.207 38.218 1 27.7 ? O3' ADP 404 A 1 HETATM 15 C C2' ADP . . . E 5 22.471 17.13 40.256 1 26.77 ? C2' ADP 404 A 1 HETATM 16 O O2' ADP . . . E 5 22.516 18.419 40.886 1 29.4 ? O2' ADP 404 A 1 HETATM 17 C C1' ADP . . . E 5 21.1 16.805 39.72 1 22.23 ? C1' ADP 404 A 1 HETATM 18 N N9 ADP . . . E 5 20.126 16.37 40.742 1 24.49 ? N9 ADP 404 A 1 HETATM 19 C C8 ADP . . . E 5 20.19 15.218 41.461 1 24.62 ? C8 ADP 404 A 1 HETATM 20 N N7 ADP . . . E 5 19.111 15.117 42.288 1 24.39 ? N7 ADP 404 A 1 HETATM 21 C C5 ADP . . . E 5 18.346 16.232 42.093 1 22.25 ? C5 ADP 404 A 1 HETATM 22 C C6 ADP . . . E 5 17.103 16.775 42.653 1 27.39 ? C6 ADP 404 A 1 HETATM 23 N N6 ADP . . . E 5 16.378 16.078 43.606 1 25.37 ? N6 ADP 404 A 1 HETATM 24 N N1 ADP . . . E 5 16.685 17.969 42.142 1 27.95 ? N1 ADP 404 A 1 HETATM 25 C C2 ADP . . . E 5 17.366 18.671 41.206 1 30.82 ? C2 ADP 404 A 1 HETATM 26 N N3 ADP . . . E 5 18.534 18.222 40.685 1 25.39 ? N3 ADP 404 A 1 HETATM 27 C C4 ADP . . . E 5 19.031 17.038 41.078 1 22.86 ? C4 ADP 404 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 23 _model_server_stats.element_count 27 #