data_5OSE # _model_server_result.job_id DRPXZcwKBNk1aIPcPbqkoA _model_server_result.datetime_utc '2024-11-27 12:08:16' _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 5ose # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5OSE # _exptl.entry_id 5OSE _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 5OSE _cell.length_a 81.97 _cell.length_b 81.97 _cell.length_c 175.26 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OSE _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C TPO 162 A TPO 288 1_555 A N LEU 163 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OD1 ASN 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc3 A OD1 ASP 148 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc7 C MG MG . A MG 402 1_555 F O HOH . A HOH 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc8 C MG MG . A MG 402 1_555 F O HOH . A HOH 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc9 D MG MG . A MG 403 1_555 F O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc10 D MG MG . A MG 403 1_555 F O HOH . A HOH 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc11 D MG MG . A MG 403 1_555 F O HOH . A HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc12 D MG MG . A MG 403 1_555 F O HOH . A HOH 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _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 23 n n PB O2B ADP sing 24 n n PB O3B ADP sing 25 n n PB O3A ADP sing 26 n n O2B HOB2 ADP sing 27 n n O3B HOB3 ADP sing 28 n n PA O1A ADP doub 29 n n PA O2A ADP sing 30 n n PA O3A ADP sing 31 n n PA O5' ADP sing 32 n n O2A HOA2 ADP sing 33 n n O5' C5' ADP sing 34 n n C5' C4' ADP sing 35 n n C5' "H5'1" ADP sing 36 n n C5' "H5'2" ADP sing 37 n n C4' O4' ADP sing 38 n n C4' C3' ADP sing 39 n n C4' H4' ADP sing 40 n n O4' C1' ADP sing 41 n n C3' O3' ADP sing 42 n n C3' C2' ADP sing 43 n n C3' H3' ADP sing 44 n n O3' HO3' ADP sing 45 n n C2' O2' ADP sing 46 n n C2' C1' ADP sing 47 n n C2' H2' ADP sing 48 n n O2' HO2' ADP sing 49 n n C1' N9 ADP sing 50 n n C1' H1' ADP sing 51 n n N9 C8 ADP sing 52 n y N9 C4 ADP sing 53 n y C8 N7 ADP doub 54 n y C8 H8 ADP sing 55 n n N7 C5 ADP sing 56 n y C5 C6 ADP sing 57 n y C5 C4 ADP doub 58 n y C6 N6 ADP sing 59 n n C6 N1 ADP doub 60 n y N6 HN61 ADP sing 61 n n N6 HN62 ADP sing 62 n n N1 C2 ADP sing 63 n y C2 N3 ADP doub 64 n y C2 H2 ADP sing 65 n n N3 C4 ADP sing 66 n y # _atom_sites.entry_id 5OSE _atom_sites.fract_transf_matrix[1][1] 0.0122 _atom_sites.fract_transf_matrix[1][2] 0.007043 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014087 _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] 0.005706 _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 A98 A 1 404 1 A98 FRG . F 5 HOH A 1 501 48 HOH HOH . F 5 HOH A 2 502 5 HOH HOH . F 5 HOH A 3 503 96 HOH HOH . F 5 HOH A 4 504 39 HOH HOH . F 5 HOH A 5 505 72 HOH HOH . F 5 HOH A 6 506 88 HOH HOH . F 5 HOH A 7 507 116 HOH HOH . F 5 HOH A 8 508 58 HOH HOH . F 5 HOH A 9 509 64 HOH HOH . F 5 HOH A 10 510 61 HOH HOH . F 5 HOH A 11 511 6 HOH HOH . F 5 HOH A 12 512 97 HOH HOH . F 5 HOH A 13 513 77 HOH HOH . F 5 HOH A 14 514 25 HOH HOH . F 5 HOH A 15 515 62 HOH HOH . F 5 HOH A 16 516 101 HOH HOH . F 5 HOH A 17 517 79 HOH HOH . F 5 HOH A 18 518 7 HOH HOH . F 5 HOH A 19 519 16 HOH HOH . F 5 HOH A 20 520 46 HOH HOH . F 5 HOH A 21 521 71 HOH HOH . F 5 HOH A 22 522 55 HOH HOH . F 5 HOH A 23 523 10 HOH HOH . F 5 HOH A 24 524 14 HOH HOH . F 5 HOH A 25 525 49 HOH HOH . F 5 HOH A 26 526 34 HOH HOH . F 5 HOH A 27 527 13 HOH HOH . F 5 HOH A 28 528 56 HOH HOH . F 5 HOH A 29 529 1 HOH HOH . F 5 HOH A 30 530 43 HOH HOH . F 5 HOH A 31 531 47 HOH HOH . F 5 HOH A 32 532 15 HOH HOH . F 5 HOH A 33 533 33 HOH HOH . F 5 HOH A 34 534 20 HOH HOH . F 5 HOH A 35 535 65 HOH HOH . F 5 HOH A 36 536 73 HOH HOH . F 5 HOH A 37 537 24 HOH HOH . F 5 HOH A 38 538 19 HOH HOH . F 5 HOH A 39 539 30 HOH HOH . F 5 HOH A 40 540 45 HOH HOH . F 5 HOH A 41 541 11 HOH HOH . F 5 HOH A 42 542 31 HOH HOH . F 5 HOH A 43 543 94 HOH HOH . F 5 HOH A 44 544 4 HOH HOH . F 5 HOH A 45 545 22 HOH HOH . F 5 HOH A 46 546 100 HOH HOH . F 5 HOH A 47 547 12 HOH HOH . F 5 HOH A 48 548 36 HOH HOH . F 5 HOH A 49 549 21 HOH HOH . F 5 HOH A 50 550 8 HOH HOH . F 5 HOH A 51 551 80 HOH HOH . F 5 HOH A 52 552 54 HOH HOH . F 5 HOH A 53 553 37 HOH HOH . F 5 HOH A 54 554 40 HOH HOH . F 5 HOH A 55 555 57 HOH HOH . F 5 HOH A 56 556 90 HOH HOH . F 5 HOH A 57 557 82 HOH HOH . F 5 HOH A 58 558 95 HOH HOH . F 5 HOH A 59 559 9 HOH HOH . F 5 HOH A 60 560 32 HOH HOH . F 5 HOH A 61 561 23 HOH HOH . F 5 HOH A 62 562 26 HOH HOH . F 5 HOH A 63 563 28 HOH HOH . F 5 HOH A 64 564 17 HOH HOH . F 5 HOH A 65 565 27 HOH HOH . F 5 HOH A 66 566 87 HOH HOH . F 5 HOH A 67 567 2 HOH HOH . F 5 HOH A 68 568 74 HOH HOH . F 5 HOH A 69 569 38 HOH HOH . F 5 HOH A 70 570 35 HOH HOH . F 5 HOH A 71 571 52 HOH HOH . F 5 HOH A 72 572 83 HOH HOH . F 5 HOH A 73 573 86 HOH HOH . F 5 HOH A 74 574 51 HOH HOH . F 5 HOH A 75 575 3 HOH HOH . F 5 HOH A 76 576 60 HOH HOH . F 5 HOH A 77 577 18 HOH HOH . F 5 HOH A 78 578 59 HOH HOH . F 5 HOH A 79 579 103 HOH HOH . F 5 HOH A 80 580 75 HOH HOH . F 5 HOH A 81 581 70 HOH HOH . F 5 HOH A 82 582 66 HOH HOH . F 5 HOH A 83 583 68 HOH HOH . F 5 HOH A 84 584 63 HOH HOH . F 5 HOH A 85 585 50 HOH HOH . F 5 HOH A 86 586 44 HOH HOH . F 5 HOH A 87 587 81 HOH HOH . F 5 HOH A 88 588 99 HOH HOH . F 5 HOH A 89 589 42 HOH HOH . F 5 HOH A 90 590 29 HOH HOH . F 5 HOH A 91 591 93 HOH HOH . F 5 HOH A 92 592 85 HOH HOH . F 5 HOH A 93 593 84 HOH HOH . F 5 HOH A 94 594 109 HOH HOH . F 5 HOH A 95 595 89 HOH HOH . F 5 HOH A 96 596 53 HOH HOH . F 5 HOH A 97 597 102 HOH HOH . F 5 HOH A 98 598 108 HOH HOH . F 5 HOH A 99 599 115 HOH HOH . F 5 HOH A 100 600 76 HOH HOH . F 5 HOH A 101 601 41 HOH HOH . F 5 HOH A 102 602 112 HOH HOH . F 5 HOH A 103 603 117 HOH HOH . F 5 HOH A 104 604 92 HOH HOH . F 5 HOH A 105 605 114 HOH HOH . F 5 HOH A 106 606 106 HOH HOH . F 5 HOH A 107 607 113 HOH HOH . F 5 HOH A 108 608 67 HOH HOH . F 5 HOH A 109 609 78 HOH HOH . F 5 HOH A 110 610 107 HOH HOH . F 5 HOH A 111 611 69 HOH HOH . F 5 HOH A 112 612 104 HOH HOH . F 5 HOH A 113 613 111 HOH HOH . F 5 HOH A 114 614 105 HOH HOH . F 5 HOH A 115 615 91 HOH HOH . F 5 HOH A 116 616 98 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 -12.288 24.079 -5.972 1 43.11 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -12.94 23.709 -7.275 1 41.18 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -11.719 22.881 -5.249 1 43.1 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -13.097 25.023 -5.114 1 41.64 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -10.896 26.397 -7.028 1 37.27 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -10.692 26.365 -8.52 1 41.04 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -12.002 27.234 -6.439 1 39.82 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -10.959 24.903 -6.392 1 38.67 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.512 26.938 -6.39 1 38.55 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.3 26.805 -4.981 1 40.13 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.529 27.988 -4.406 1 37.03 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -7.229 28.109 -4.999 1 38.12 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -9.229 29.311 -4.674 1 38.44 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.185 29.626 -3.657 1 36.16 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -8.071 30.285 -4.702 1 37.83 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -7.717 30.613 -3.359 1 38.06 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -6.923 29.481 -5.271 1 33.61 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -6.864 29.669 -6.74 1 34.84 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.569 28.946 -7.634 1 37.3 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.305 29.348 -8.9 1 34.47 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.409 30.35 -8.823 1 35.75 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -5.71 31.208 -9.802 1 39.16 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -5.941 31.055 -11.131 1 38.3 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -4.852 32.139 -9.321 1 40.81 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.632 32.283 -7.997 1 38.13 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -5.231 31.533 -7.049 1 35.31 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.119 30.563 -7.396 1 33.45 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #