data_5OS0 # _model_server_result.job_id 7FH6DEpN-E1GHVlabDYcXA _model_server_result.datetime_utc '2025-07-13 04:10:01' _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 5os0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5OS0 # _exptl.entry_id 5OS0 _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 90 _cell.angle_gamma 120 _cell.entry_id 5OS0 _cell.length_a 82.21 _cell.length_b 82.21 _cell.length_c 175.86 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OS0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 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 161 A THR 287 1_555 A N TPO 162 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C TPO 162 A TPO 288 1_555 A N LEU 163 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? metalc ? metalc1 A OD1 ASN 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc3 A OD1 ASP 148 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc7 C MG MG . A MG 402 1_555 F O HOH . A HOH 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc8 C MG MG . A MG 402 1_555 F O HOH . A HOH 595 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc9 D MG MG . A MG 403 1_555 F O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc10 D MG MG . A MG 403 1_555 F O HOH . A HOH 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc11 D MG MG . A MG 403 1_555 F O HOH . A HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc12 D MG MG . A MG 403 1_555 F O HOH . A HOH 624 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? # _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 33 n n PB O2B ADP sing 34 n n PB O3B ADP sing 35 n n PB O3A ADP sing 36 n n O2B HOB2 ADP sing 37 n n O3B HOB3 ADP sing 38 n n PA O1A ADP doub 39 n n PA O2A ADP sing 40 n n PA O3A ADP sing 41 n n PA O5' ADP sing 42 n n O2A HOA2 ADP sing 43 n n O5' C5' ADP sing 44 n n C5' C4' ADP sing 45 n n C5' "H5'1" ADP sing 46 n n C5' "H5'2" ADP sing 47 n n C4' O4' ADP sing 48 n n C4' C3' ADP sing 49 n n C4' H4' ADP sing 50 n n O4' C1' ADP sing 51 n n C3' O3' ADP sing 52 n n C3' C2' ADP sing 53 n n C3' H3' ADP sing 54 n n O3' HO3' ADP sing 55 n n C2' O2' ADP sing 56 n n C2' C1' ADP sing 57 n n C2' H2' ADP sing 58 n n O2' HO2' ADP sing 59 n n C1' N9 ADP sing 60 n n C1' H1' ADP sing 61 n n N9 C8 ADP sing 62 n y N9 C4 ADP sing 63 n y C8 N7 ADP doub 64 n y C8 H8 ADP sing 65 n n N7 C5 ADP sing 66 n y C5 C6 ADP sing 67 n y C5 C4 ADP doub 68 n y C6 N6 ADP sing 69 n n C6 N1 ADP doub 70 n y N6 HN61 ADP sing 71 n n N6 HN62 ADP sing 72 n n N1 C2 ADP sing 73 n y C2 N3 ADP doub 74 n y C2 H2 ADP sing 75 n n N3 C4 ADP sing 76 n y # _atom_sites.entry_id 5OS0 _atom_sites.fract_transf_matrix[1][1] 0.012164 _atom_sites.fract_transf_matrix[1][2] 0.007023 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014046 _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] 0.005686 _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 1392 ADP ADP . C 3 MG A 1 402 1395 MG MG . D 3 MG A 1 403 1396 MG MG . E 4 A6Z A 1 404 1 A6Z FRG . F 5 HOH A 1 501 6 HOH HOH . F 5 HOH A 2 502 57 HOH HOH . F 5 HOH A 3 503 75 HOH HOH . F 5 HOH A 4 504 111 HOH HOH . F 5 HOH A 5 505 127 HOH HOH . F 5 HOH A 6 506 83 HOH HOH . F 5 HOH A 7 507 93 HOH HOH . F 5 HOH A 8 508 45 HOH HOH . F 5 HOH A 9 509 130 HOH HOH . F 5 HOH A 10 510 7 HOH HOH . F 5 HOH A 11 511 110 HOH HOH . F 5 HOH A 12 512 2 HOH HOH . F 5 HOH A 13 513 108 HOH HOH . F 5 HOH A 14 514 100 HOH HOH . F 5 HOH A 15 515 96 HOH HOH . F 5 HOH A 16 516 70 HOH HOH . F 5 HOH A 17 517 17 HOH HOH . F 5 HOH A 18 518 133 HOH HOH . F 5 HOH A 19 519 62 HOH HOH . F 5 HOH A 20 520 78 HOH HOH . F 5 HOH A 21 521 121 HOH HOH . F 5 HOH A 22 522 138 HOH HOH . F 5 HOH A 23 523 72 HOH HOH . F 5 HOH A 24 524 53 HOH HOH . F 5 HOH A 25 525 39 HOH HOH . F 5 HOH A 26 526 29 HOH HOH . F 5 HOH A 27 527 12 HOH HOH . F 5 HOH A 28 528 9 HOH HOH . F 5 HOH A 29 529 21 HOH HOH . F 5 HOH A 30 530 107 HOH HOH . F 5 HOH A 31 531 31 HOH HOH . F 5 HOH A 32 532 18 HOH HOH . F 5 HOH A 33 533 91 HOH HOH . F 5 HOH A 34 534 40 HOH HOH . F 5 HOH A 35 535 22 HOH HOH . F 5 HOH A 36 536 143 HOH HOH . F 5 HOH A 37 537 30 HOH HOH . F 5 HOH A 38 538 61 HOH HOH . F 5 HOH A 39 539 82 HOH HOH . F 5 HOH A 40 540 69 HOH HOH . F 5 HOH A 41 541 24 HOH HOH . F 5 HOH A 42 542 131 HOH HOH . F 5 HOH A 43 543 13 HOH HOH . F 5 HOH A 44 544 124 HOH HOH . F 5 HOH A 45 545 43 HOH HOH . F 5 HOH A 46 546 87 HOH HOH . F 5 HOH A 47 547 112 HOH HOH . F 5 HOH A 48 548 27 HOH HOH . F 5 HOH A 49 549 126 HOH HOH . F 5 HOH A 50 550 92 HOH HOH . F 5 HOH A 51 551 59 HOH HOH . F 5 HOH A 52 552 51 HOH HOH . F 5 HOH A 53 553 46 HOH HOH . F 5 HOH A 54 554 37 HOH HOH . F 5 HOH A 55 555 36 HOH HOH . F 5 HOH A 56 556 42 HOH HOH . F 5 HOH A 57 557 65 HOH HOH . F 5 HOH A 58 558 15 HOH HOH . F 5 HOH A 59 559 77 HOH HOH . F 5 HOH A 60 560 136 HOH HOH . F 5 HOH A 61 561 44 HOH HOH . F 5 HOH A 62 562 16 HOH HOH . F 5 HOH A 63 563 73 HOH HOH . F 5 HOH A 64 564 134 HOH HOH . F 5 HOH A 65 565 74 HOH HOH . F 5 HOH A 66 566 94 HOH HOH . F 5 HOH A 67 567 23 HOH HOH . F 5 HOH A 68 568 34 HOH HOH . F 5 HOH A 69 569 14 HOH HOH . F 5 HOH A 70 570 49 HOH HOH . F 5 HOH A 71 571 5 HOH HOH . F 5 HOH A 72 572 1 HOH HOH . F 5 HOH A 73 573 141 HOH HOH . F 5 HOH A 74 574 85 HOH HOH . F 5 HOH A 75 575 123 HOH HOH . F 5 HOH A 76 576 26 HOH HOH . F 5 HOH A 77 577 68 HOH HOH . F 5 HOH A 78 578 25 HOH HOH . F 5 HOH A 79 579 10 HOH HOH . F 5 HOH A 80 580 140 HOH HOH . F 5 HOH A 81 581 117 HOH HOH . F 5 HOH A 82 582 99 HOH HOH . F 5 HOH A 83 583 71 HOH HOH . F 5 HOH A 84 584 11 HOH HOH . F 5 HOH A 85 585 64 HOH HOH . F 5 HOH A 86 586 76 HOH HOH . F 5 HOH A 87 587 79 HOH HOH . F 5 HOH A 88 588 80 HOH HOH . F 5 HOH A 89 589 3 HOH HOH . F 5 HOH A 90 590 19 HOH HOH . F 5 HOH A 91 591 33 HOH HOH . F 5 HOH A 92 592 105 HOH HOH . F 5 HOH A 93 593 120 HOH HOH . F 5 HOH A 94 594 97 HOH HOH . F 5 HOH A 95 595 32 HOH HOH . F 5 HOH A 96 596 56 HOH HOH . F 5 HOH A 97 597 4 HOH HOH . F 5 HOH A 98 598 38 HOH HOH . F 5 HOH A 99 599 63 HOH HOH . F 5 HOH A 100 600 101 HOH HOH . F 5 HOH A 101 601 95 HOH HOH . F 5 HOH A 102 602 50 HOH HOH . F 5 HOH A 103 603 142 HOH HOH . F 5 HOH A 104 604 54 HOH HOH . F 5 HOH A 105 605 28 HOH HOH . F 5 HOH A 106 606 41 HOH HOH . F 5 HOH A 107 607 86 HOH HOH . F 5 HOH A 108 608 114 HOH HOH . F 5 HOH A 109 609 135 HOH HOH . F 5 HOH A 110 610 89 HOH HOH . F 5 HOH A 111 611 20 HOH HOH . F 5 HOH A 112 612 48 HOH HOH . F 5 HOH A 113 613 102 HOH HOH . F 5 HOH A 114 614 67 HOH HOH . F 5 HOH A 115 615 144 HOH HOH . F 5 HOH A 116 616 88 HOH HOH . F 5 HOH A 117 617 118 HOH HOH . F 5 HOH A 118 618 125 HOH HOH . F 5 HOH A 119 619 8 HOH HOH . F 5 HOH A 120 620 90 HOH HOH . F 5 HOH A 121 621 122 HOH HOH . F 5 HOH A 122 622 35 HOH HOH . F 5 HOH A 123 623 119 HOH HOH . F 5 HOH A 124 624 52 HOH HOH . F 5 HOH A 125 625 103 HOH HOH . F 5 HOH A 126 626 128 HOH HOH . F 5 HOH A 127 627 116 HOH HOH . F 5 HOH A 128 628 129 HOH HOH . F 5 HOH A 129 629 109 HOH HOH . F 5 HOH A 130 630 132 HOH HOH . F 5 HOH A 131 631 113 HOH HOH . F 5 HOH A 132 632 98 HOH HOH . F 5 HOH A 133 633 47 HOH HOH . F 5 HOH A 134 634 115 HOH HOH . F 5 HOH A 135 635 84 HOH HOH . F 5 HOH A 136 636 106 HOH HOH . F 5 HOH A 137 637 104 HOH HOH . F 5 HOH A 138 638 55 HOH HOH . F 5 HOH A 139 639 137 HOH HOH . F 5 HOH A 140 640 81 HOH HOH . F 5 HOH A 141 641 139 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 -12.413 24.223 -6.01 1 35.26 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -13.104 23.8 -7.285 1 33.18 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -11.852 23.025 -5.292 1 37.35 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -13.206 25.197 -5.146 1 33.03 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -11.007 26.582 -7.086 1 29.95 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -10.77 26.663 -8.574 1 35.08 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -12.122 27.483 -6.579 1 31.99 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -11.116 25.077 -6.535 1 31.23 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.586 27.084 -6.481 1 30.27 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.428 27.039 -5.049 1 34.42 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.644 28.239 -4.507 1 30.96 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -7.328 28.363 -5.097 1 30.74 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -9.319 29.576 -4.77 1 30.93 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.397 29.795 -3.831 1 30.56 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -8.133 30.518 -4.647 1 31.92 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -7.763 30.639 -3.259 1 31.16 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -7.007 29.736 -5.306 1 27.68 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -6.987 29.939 -6.782 1 28.92 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.709 29.191 -7.652 1 29.98 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.46 29.581 -8.921 1 29.9 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.553 30.588 -8.884 1 29.3 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -5.874 31.431 -9.889 1 33.11 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -6.136 31.275 -11.221 1 31.53 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -5 32.375 -9.444 1 31.09 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.756 32.538 -8.123 1 31.5 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -5.339 31.798 -7.154 1 28.26 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.246 30.82 -7.47 1 29.31 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #