data_5OSD # _model_server_result.job_id 1vA0xE_bafsegVPtFtqZlQ _model_server_result.datetime_utc '2024-11-27 04:10:24' _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 5osd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5OSD # _exptl.entry_id 5OSD _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 5OSD _cell.length_a 81.95 _cell.length_b 81.95 _cell.length_c 175.35 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OSD _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,G,H,I _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 163 A THR 287 1_555 A N TPO 164 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 164 A TPO 288 1_555 A N LEU 165 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD1 ASN 137 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 A OD2 ASP 150 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc3 A OD1 ASP 150 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc7 C MG MG . A MG 402 1_555 I O HOH . A HOH 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc8 C MG MG . A MG 402 1_555 I O HOH . A HOH 561 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc9 D MG MG . A MG 403 1_555 I O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc10 D MG MG . A MG 403 1_555 I O HOH . A HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc11 D MG MG . A MG 403 1_555 I O HOH . A HOH 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc12 D MG MG . A MG 403 1_555 I O HOH . A HOH 587 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? # _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 27 n n PB O2B ADP sing 28 n n PB O3B ADP sing 29 n n PB O3A ADP sing 30 n n O2B HOB2 ADP sing 31 n n O3B HOB3 ADP sing 32 n n PA O1A ADP doub 33 n n PA O2A ADP sing 34 n n PA O3A ADP sing 35 n n PA O5' ADP sing 36 n n O2A HOA2 ADP sing 37 n n O5' C5' ADP sing 38 n n C5' C4' ADP sing 39 n n C5' "H5'1" ADP sing 40 n n C5' "H5'2" ADP sing 41 n n C4' O4' ADP sing 42 n n C4' C3' ADP sing 43 n n C4' H4' ADP sing 44 n n O4' C1' ADP sing 45 n n C3' O3' ADP sing 46 n n C3' C2' ADP sing 47 n n C3' H3' ADP sing 48 n n O3' HO3' ADP sing 49 n n C2' O2' ADP sing 50 n n C2' C1' ADP sing 51 n n C2' H2' ADP sing 52 n n O2' HO2' ADP sing 53 n n C1' N9 ADP sing 54 n n C1' H1' ADP sing 55 n n N9 C8 ADP sing 56 n y N9 C4 ADP sing 57 n y C8 N7 ADP doub 58 n y C8 H8 ADP sing 59 n n N7 C5 ADP sing 60 n y C5 C6 ADP sing 61 n y C5 C4 ADP doub 62 n y C6 N6 ADP sing 63 n n C6 N1 ADP doub 64 n y N6 HN61 ADP sing 65 n n N6 HN62 ADP sing 66 n n N1 C2 ADP sing 67 n y C2 N3 ADP doub 68 n y C2 H2 ADP sing 69 n n N3 C4 ADP sing 70 n y # _atom_sites.entry_id 5OSD _atom_sites.fract_transf_matrix[1][1] 0.012203 _atom_sites.fract_transf_matrix[1][2] 0.007045 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01409 _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] 0.005703 _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 A9B A 1 404 1 A9B FRG . F 5 CL A 1 405 1 CL CL . G 5 CL A 1 406 2 CL CL . H 5 CL A 1 407 3 CL CL . I 6 HOH A 1 501 51 HOH HOH . I 6 HOH A 2 502 6 HOH HOH . I 6 HOH A 3 503 40 HOH HOH . I 6 HOH A 4 504 7 HOH HOH . I 6 HOH A 5 505 54 HOH HOH . I 6 HOH A 6 506 64 HOH HOH . I 6 HOH A 7 507 49 HOH HOH . I 6 HOH A 8 508 50 HOH HOH . I 6 HOH A 9 509 48 HOH HOH . I 6 HOH A 10 510 12 HOH HOH . I 6 HOH A 11 511 93 HOH HOH . I 6 HOH A 12 512 1 HOH HOH . I 6 HOH A 13 513 20 HOH HOH . I 6 HOH A 14 514 53 HOH HOH . I 6 HOH A 15 515 5 HOH HOH . I 6 HOH A 16 516 26 HOH HOH . I 6 HOH A 17 517 70 HOH HOH . I 6 HOH A 18 518 35 HOH HOH . I 6 HOH A 19 519 16 HOH HOH . I 6 HOH A 20 520 17 HOH HOH . I 6 HOH A 21 521 2 HOH HOH . I 6 HOH A 22 522 79 HOH HOH . I 6 HOH A 23 523 25 HOH HOH . I 6 HOH A 24 524 19 HOH HOH . I 6 HOH A 25 525 14 HOH HOH . I 6 HOH A 26 526 11 HOH HOH . I 6 HOH A 27 527 32 HOH HOH . I 6 HOH A 28 528 8 HOH HOH . I 6 HOH A 29 529 99 HOH HOH . I 6 HOH A 30 530 102 HOH HOH . I 6 HOH A 31 531 94 HOH HOH . I 6 HOH A 32 532 31 HOH HOH . I 6 HOH A 33 533 89 HOH HOH . I 6 HOH A 34 534 37 HOH HOH . I 6 HOH A 35 535 108 HOH HOH . I 6 HOH A 36 536 13 HOH HOH . I 6 HOH A 37 537 65 HOH HOH . I 6 HOH A 38 538 21 HOH HOH . I 6 HOH A 39 539 33 HOH HOH . I 6 HOH A 40 540 45 HOH HOH . I 6 HOH A 41 541 39 HOH HOH . I 6 HOH A 42 542 38 HOH HOH . I 6 HOH A 43 543 28 HOH HOH . I 6 HOH A 44 544 57 HOH HOH . I 6 HOH A 45 545 34 HOH HOH . I 6 HOH A 46 546 22 HOH HOH . I 6 HOH A 47 547 15 HOH HOH . I 6 HOH A 48 548 29 HOH HOH . I 6 HOH A 49 549 23 HOH HOH . I 6 HOH A 50 550 24 HOH HOH . I 6 HOH A 51 551 36 HOH HOH . I 6 HOH A 52 552 113 HOH HOH . I 6 HOH A 53 553 69 HOH HOH . I 6 HOH A 54 554 55 HOH HOH . I 6 HOH A 55 555 9 HOH HOH . I 6 HOH A 56 556 10 HOH HOH . I 6 HOH A 57 557 110 HOH HOH . I 6 HOH A 58 558 41 HOH HOH . I 6 HOH A 59 559 46 HOH HOH . I 6 HOH A 60 560 71 HOH HOH . I 6 HOH A 61 561 80 HOH HOH . I 6 HOH A 62 562 68 HOH HOH . I 6 HOH A 63 563 47 HOH HOH . I 6 HOH A 64 564 59 HOH HOH . I 6 HOH A 65 565 104 HOH HOH . I 6 HOH A 66 566 3 HOH HOH . I 6 HOH A 67 567 81 HOH HOH . I 6 HOH A 68 568 4 HOH HOH . I 6 HOH A 69 569 75 HOH HOH . I 6 HOH A 70 570 18 HOH HOH . I 6 HOH A 71 571 83 HOH HOH . I 6 HOH A 72 572 30 HOH HOH . I 6 HOH A 73 573 91 HOH HOH . I 6 HOH A 74 574 84 HOH HOH . I 6 HOH A 75 575 77 HOH HOH . I 6 HOH A 76 576 58 HOH HOH . I 6 HOH A 77 577 61 HOH HOH . I 6 HOH A 78 578 44 HOH HOH . I 6 HOH A 79 579 107 HOH HOH . I 6 HOH A 80 580 52 HOH HOH . I 6 HOH A 81 581 56 HOH HOH . I 6 HOH A 82 582 103 HOH HOH . I 6 HOH A 83 583 73 HOH HOH . I 6 HOH A 84 584 76 HOH HOH . I 6 HOH A 85 585 114 HOH HOH . I 6 HOH A 86 586 66 HOH HOH . I 6 HOH A 87 587 116 HOH HOH . I 6 HOH A 88 588 82 HOH HOH . I 6 HOH A 89 589 106 HOH HOH . I 6 HOH A 90 590 97 HOH HOH . I 6 HOH A 91 591 111 HOH HOH . I 6 HOH A 92 592 117 HOH HOH . I 6 HOH A 93 593 105 HOH HOH . I 6 HOH A 94 594 109 HOH HOH . I 6 HOH A 95 595 112 HOH HOH . I 6 HOH A 96 596 115 HOH HOH . I 6 HOH A 97 597 101 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 -12.205 24.056 -6.033 1 47.02 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -12.801 23.856 -7.404 1 49.28 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -11.714 22.78 -5.393 1 47.72 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -13.014 24.945 -5.12 1 41.13 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -10.802 26.336 -6.994 1 38.49 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -10.625 26.207 -8.488 1 46.76 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -11.932 27.163 -6.428 1 40.81 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -10.842 24.881 -6.3 1 46.89 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.435 26.914 -6.367 1 39.62 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.217 26.77 -4.964 1 37.77 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.431 27.952 -4.41 1 32.99 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -7.155 28.075 -5.045 1 36.04 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -9.148 29.268 -4.649 1 36.96 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.032 29.582 -3.569 1 38 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -8.01 30.257 -4.751 1 41.19 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -7.657 30.682 -3.433 1 38.44 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -6.854 29.448 -5.311 1 35.04 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -6.792 29.641 -6.782 1 33.22 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.486 28.916 -7.681 1 40.1 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.226 29.319 -8.948 1 37.52 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.342 30.33 -8.874 1 39.25 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -5.649 31.207 -9.846 1 42 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -5.86 31.072 -11.18 1 39.8 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -4.803 32.142 -9.36 1 35.17 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.589 32.28 -8.035 1 36.99 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -5.184 31.519 -7.097 1 35.21 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.057 30.542 -7.444 1 34.87 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #