data_5OS3 # _model_server_result.job_id fDQXK_4e99KGGbSK_RGj8A _model_server_result.datetime_utc '2025-04-13 04:05:43' _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 5os3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5OS3 # _exptl.entry_id 5OS3 _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 5OS3 _cell.length_a 81.86 _cell.length_b 81.86 _cell.length_c 176.45 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OS3 _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OD1 ASN 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc3 A OD1 ASP 148 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc7 C MG MG . A MG 402 1_555 F O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc8 C MG MG . A MG 402 1_555 F O HOH . A HOH 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc9 D MG MG . A MG 403 1_555 F O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc10 D MG MG . A MG 403 1_555 F O HOH . A HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc11 D MG MG . A MG 403 1_555 F O HOH . A HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc12 D MG MG . A MG 403 1_555 F O HOH . A HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? # _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 28 n n PB O2B ADP sing 29 n n PB O3B ADP sing 30 n n PB O3A ADP sing 31 n n O2B HOB2 ADP sing 32 n n O3B HOB3 ADP sing 33 n n PA O1A ADP doub 34 n n PA O2A ADP sing 35 n n PA O3A ADP sing 36 n n PA O5' ADP sing 37 n n O2A HOA2 ADP sing 38 n n O5' C5' ADP sing 39 n n C5' C4' ADP sing 40 n n C5' "H5'1" ADP sing 41 n n C5' "H5'2" ADP sing 42 n n C4' O4' ADP sing 43 n n C4' C3' ADP sing 44 n n C4' H4' ADP sing 45 n n O4' C1' ADP sing 46 n n C3' O3' ADP sing 47 n n C3' C2' ADP sing 48 n n C3' H3' ADP sing 49 n n O3' HO3' ADP sing 50 n n C2' O2' ADP sing 51 n n C2' C1' ADP sing 52 n n C2' H2' ADP sing 53 n n O2' HO2' ADP sing 54 n n C1' N9 ADP sing 55 n n C1' H1' ADP sing 56 n n N9 C8 ADP sing 57 n y N9 C4 ADP sing 58 n y C8 N7 ADP doub 59 n y C8 H8 ADP sing 60 n n N7 C5 ADP sing 61 n y C5 C6 ADP sing 62 n y C5 C4 ADP doub 63 n y C6 N6 ADP sing 64 n n C6 N1 ADP doub 65 n y N6 HN61 ADP sing 66 n n N6 HN62 ADP sing 67 n n N1 C2 ADP sing 68 n y C2 N3 ADP doub 69 n y C2 H2 ADP sing 70 n n N3 C4 ADP sing 71 n y # _atom_sites.entry_id 5OS3 _atom_sites.fract_transf_matrix[1][1] 0.012216 _atom_sites.fract_transf_matrix[1][2] 0.007053 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014106 _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] 0.005667 _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 A7N A 1 404 1 A7N FRG . F 5 HOH A 1 501 82 HOH HOH . F 5 HOH A 2 502 88 HOH HOH . F 5 HOH A 3 503 122 HOH HOH . F 5 HOH A 4 504 119 HOH HOH . F 5 HOH A 5 505 48 HOH HOH . F 5 HOH A 6 506 131 HOH HOH . F 5 HOH A 7 507 6 HOH HOH . F 5 HOH A 8 508 81 HOH HOH . F 5 HOH A 9 509 114 HOH HOH . F 5 HOH A 10 510 105 HOH HOH . F 5 HOH A 11 511 107 HOH HOH . F 5 HOH A 12 512 136 HOH HOH . F 5 HOH A 13 513 96 HOH HOH . F 5 HOH A 14 514 51 HOH HOH . F 5 HOH A 15 515 137 HOH HOH . F 5 HOH A 16 516 79 HOH HOH . F 5 HOH A 17 517 20 HOH HOH . F 5 HOH A 18 518 92 HOH HOH . F 5 HOH A 19 519 108 HOH HOH . F 5 HOH A 20 520 72 HOH HOH . F 5 HOH A 21 521 83 HOH HOH . F 5 HOH A 22 522 61 HOH HOH . F 5 HOH A 23 523 139 HOH HOH . F 5 HOH A 24 524 121 HOH HOH . F 5 HOH A 25 525 68 HOH HOH . F 5 HOH A 26 526 24 HOH HOH . F 5 HOH A 27 527 26 HOH HOH . F 5 HOH A 28 528 54 HOH HOH . F 5 HOH A 29 529 2 HOH HOH . F 5 HOH A 30 530 143 HOH HOH . F 5 HOH A 31 531 41 HOH HOH . F 5 HOH A 32 532 42 HOH HOH . F 5 HOH A 33 533 1 HOH HOH . F 5 HOH A 34 534 19 HOH HOH . F 5 HOH A 35 535 31 HOH HOH . F 5 HOH A 36 536 30 HOH HOH . F 5 HOH A 37 537 73 HOH HOH . F 5 HOH A 38 538 87 HOH HOH . F 5 HOH A 39 539 85 HOH HOH . F 5 HOH A 40 540 39 HOH HOH . F 5 HOH A 41 541 140 HOH HOH . F 5 HOH A 42 542 115 HOH HOH . F 5 HOH A 43 543 100 HOH HOH . F 5 HOH A 44 544 102 HOH HOH . F 5 HOH A 45 545 98 HOH HOH . F 5 HOH A 46 546 99 HOH HOH . F 5 HOH A 47 547 17 HOH HOH . F 5 HOH A 48 548 97 HOH HOH . F 5 HOH A 49 549 25 HOH HOH . F 5 HOH A 50 550 116 HOH HOH . F 5 HOH A 51 551 95 HOH HOH . F 5 HOH A 52 552 57 HOH HOH . F 5 HOH A 53 553 27 HOH HOH . F 5 HOH A 54 554 16 HOH HOH . F 5 HOH A 55 555 110 HOH HOH . F 5 HOH A 56 556 38 HOH HOH . F 5 HOH A 57 557 59 HOH HOH . F 5 HOH A 58 558 49 HOH HOH . F 5 HOH A 59 559 15 HOH HOH . F 5 HOH A 60 560 103 HOH HOH . F 5 HOH A 61 561 18 HOH HOH . F 5 HOH A 62 562 63 HOH HOH . F 5 HOH A 63 563 23 HOH HOH . F 5 HOH A 64 564 13 HOH HOH . F 5 HOH A 65 565 7 HOH HOH . F 5 HOH A 66 566 28 HOH HOH . F 5 HOH A 67 567 5 HOH HOH . F 5 HOH A 68 568 33 HOH HOH . F 5 HOH A 69 569 43 HOH HOH . F 5 HOH A 70 570 47 HOH HOH . F 5 HOH A 71 571 10 HOH HOH . F 5 HOH A 72 572 46 HOH HOH . F 5 HOH A 73 573 71 HOH HOH . F 5 HOH A 74 574 32 HOH HOH . F 5 HOH A 75 575 12 HOH HOH . F 5 HOH A 76 576 44 HOH HOH . F 5 HOH A 77 577 94 HOH HOH . F 5 HOH A 78 578 123 HOH HOH . F 5 HOH A 79 579 78 HOH HOH . F 5 HOH A 80 580 29 HOH HOH . F 5 HOH A 81 581 112 HOH HOH . F 5 HOH A 82 582 64 HOH HOH . F 5 HOH A 83 583 77 HOH HOH . F 5 HOH A 84 584 45 HOH HOH . F 5 HOH A 85 585 8 HOH HOH . F 5 HOH A 86 586 11 HOH HOH . F 5 HOH A 87 587 34 HOH HOH . F 5 HOH A 88 588 74 HOH HOH . F 5 HOH A 89 589 67 HOH HOH . F 5 HOH A 90 590 40 HOH HOH . F 5 HOH A 91 591 4 HOH HOH . F 5 HOH A 92 592 35 HOH HOH . F 5 HOH A 93 593 117 HOH HOH . F 5 HOH A 94 594 129 HOH HOH . F 5 HOH A 95 595 126 HOH HOH . F 5 HOH A 96 596 76 HOH HOH . F 5 HOH A 97 597 127 HOH HOH . F 5 HOH A 98 598 154 HOH HOH . F 5 HOH A 99 599 124 HOH HOH . F 5 HOH A 100 600 3 HOH HOH . F 5 HOH A 101 601 138 HOH HOH . F 5 HOH A 102 602 91 HOH HOH . F 5 HOH A 103 603 55 HOH HOH . F 5 HOH A 104 604 106 HOH HOH . F 5 HOH A 105 605 56 HOH HOH . F 5 HOH A 106 606 104 HOH HOH . F 5 HOH A 107 607 62 HOH HOH . F 5 HOH A 108 608 65 HOH HOH . F 5 HOH A 109 609 69 HOH HOH . F 5 HOH A 110 610 58 HOH HOH . F 5 HOH A 111 611 52 HOH HOH . F 5 HOH A 112 612 84 HOH HOH . F 5 HOH A 113 613 37 HOH HOH . F 5 HOH A 114 614 80 HOH HOH . F 5 HOH A 115 615 14 HOH HOH . F 5 HOH A 116 616 75 HOH HOH . F 5 HOH A 117 617 135 HOH HOH . F 5 HOH A 118 618 21 HOH HOH . F 5 HOH A 119 619 149 HOH HOH . F 5 HOH A 120 620 130 HOH HOH . F 5 HOH A 121 621 22 HOH HOH . F 5 HOH A 122 622 152 HOH HOH . F 5 HOH A 123 623 70 HOH HOH . F 5 HOH A 124 624 145 HOH HOH . F 5 HOH A 125 625 134 HOH HOH . F 5 HOH A 126 626 9 HOH HOH . F 5 HOH A 127 627 36 HOH HOH . F 5 HOH A 128 628 53 HOH HOH . F 5 HOH A 129 629 86 HOH HOH . F 5 HOH A 130 630 125 HOH HOH . F 5 HOH A 131 631 128 HOH HOH . F 5 HOH A 132 632 113 HOH HOH . F 5 HOH A 133 633 109 HOH HOH . F 5 HOH A 134 634 151 HOH HOH . F 5 HOH A 135 635 141 HOH HOH . F 5 HOH A 136 636 144 HOH HOH . F 5 HOH A 137 637 50 HOH HOH . F 5 HOH A 138 638 148 HOH HOH . F 5 HOH A 139 639 150 HOH HOH . F 5 HOH A 140 640 89 HOH HOH . F 5 HOH A 141 641 147 HOH HOH . F 5 HOH A 142 642 146 HOH HOH . F 5 HOH A 143 643 101 HOH HOH . F 5 HOH A 144 644 120 HOH HOH . F 5 HOH A 145 645 155 HOH HOH . F 5 HOH A 146 646 90 HOH HOH . F 5 HOH A 147 647 133 HOH HOH . F 5 HOH A 148 648 132 HOH HOH . F 5 HOH A 149 649 153 HOH HOH . F 5 HOH A 150 650 156 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 -12.225 23.85 -5.95 1 36.08 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -12.916 23.439 -7.217 1 36.95 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -11.685 22.646 -5.226 1 41.25 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -12.993 24.83 -5.087 1 35.31 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -10.789 26.184 -7.044 1 31.68 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -10.579 26.208 -8.542 1 34.6 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -11.861 27.05 -6.456 1 35.69 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -10.9 24.693 -6.435 1 32.3 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.361 26.692 -6.429 1 33.59 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.109 26.546 -5.016 1 29.92 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.381 27.767 -4.43 1 28.95 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -7.083 27.949 -5.03 1 32.12 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -9.096 29.085 -4.683 1 31.32 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.14 29.355 -3.72 1 35.17 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -7.963 30.089 -4.641 1 33.94 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -7.6 30.3 -3.266 1 32.44 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -6.809 29.34 -5.276 1 27.52 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -6.757 29.52 -6.762 1 31.22 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.474 28.757 -7.623 1 29.49 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.225 29.101 -8.902 1 28.43 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.334 30.13 -8.876 1 30.94 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -5.638 30.952 -9.891 1 35.96 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -5.884 30.766 -11.213 1 33.65 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -4.77 31.909 -9.455 1 33.7 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.534 32.11 -8.145 1 30.78 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -5.115 31.393 -7.156 1 28.29 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.014 30.388 -7.46 1 28.85 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #