data_5ORY # _model_server_result.job_id ScnKVtMV6EV-dSPgcWhi4Q _model_server_result.datetime_utc '2024-11-23 16:02:24' _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 5ory # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5ORY # _exptl.entry_id 5ORY _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 5ORY _cell.length_a 82.14 _cell.length_b 82.14 _cell.length_c 176.25 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ORY _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 161 A THR 287 1_555 A N TPO 162 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 162 A TPO 288 1_555 A N LEU 163 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD1 ASN 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc3 A OD1 ASP 148 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc7 C MG MG . A MG 402 1_555 I O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc8 C MG MG . A MG 402 1_555 I O HOH . A HOH 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc9 D MG MG . A MG 403 1_555 I O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc10 D MG MG . A MG 403 1_555 I O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc11 D MG MG . A MG 403 1_555 I O HOH . A HOH 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc12 D MG MG . A MG 403 1_555 I O HOH . A HOH 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? # _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 5ORY _atom_sites.fract_transf_matrix[1][1] 0.012174 _atom_sites.fract_transf_matrix[1][2] 0.007029 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014058 _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] 0.005674 _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 CL A 1 404 1397 CL CL . F 4 CL A 1 405 1398 CL CL . G 5 AY4 A 1 406 1 AY4 FRG . H 4 CL A 1 407 1 CL CL . I 6 HOH A 1 501 5 HOH HOH . I 6 HOH A 2 502 2058 HOH HOH . I 6 HOH A 3 503 2007 HOH HOH . I 6 HOH A 4 504 2036 HOH HOH . I 6 HOH A 5 505 2042 HOH HOH . I 6 HOH A 6 506 2011 HOH HOH . I 6 HOH A 7 507 2029 HOH HOH . I 6 HOH A 8 508 2016 HOH HOH . I 6 HOH A 9 509 2050 HOH HOH . I 6 HOH A 10 510 2018 HOH HOH . I 6 HOH A 11 511 2046 HOH HOH . I 6 HOH A 12 512 2014 HOH HOH . I 6 HOH A 13 513 2003 HOH HOH . I 6 HOH A 14 514 2047 HOH HOH . I 6 HOH A 15 515 21 HOH HOH . I 6 HOH A 16 516 2019 HOH HOH . I 6 HOH A 17 517 2054 HOH HOH . I 6 HOH A 18 518 2038 HOH HOH . I 6 HOH A 19 519 2023 HOH HOH . I 6 HOH A 20 520 2057 HOH HOH . I 6 HOH A 21 521 2034 HOH HOH . I 6 HOH A 22 522 2068 HOH HOH . I 6 HOH A 23 523 2017 HOH HOH . I 6 HOH A 24 524 2013 HOH HOH . I 6 HOH A 25 525 19 HOH HOH . I 6 HOH A 26 526 2032 HOH HOH . I 6 HOH A 27 527 2012 HOH HOH . I 6 HOH A 28 528 2039 HOH HOH . I 6 HOH A 29 529 2052 HOH HOH . I 6 HOH A 30 530 2048 HOH HOH . I 6 HOH A 31 531 2033 HOH HOH . I 6 HOH A 32 532 2067 HOH HOH . I 6 HOH A 33 533 2006 HOH HOH . I 6 HOH A 34 534 2040 HOH HOH . I 6 HOH A 35 535 2051 HOH HOH . I 6 HOH A 36 536 2026 HOH HOH . I 6 HOH A 37 537 2059 HOH HOH . I 6 HOH A 38 538 15 HOH HOH . I 6 HOH A 39 539 2030 HOH HOH . I 6 HOH A 40 540 2028 HOH HOH . I 6 HOH A 41 541 25 HOH HOH . I 6 HOH A 42 542 18 HOH HOH . I 6 HOH A 43 543 2035 HOH HOH . I 6 HOH A 44 544 2055 HOH HOH . I 6 HOH A 45 545 2041 HOH HOH . I 6 HOH A 46 546 2045 HOH HOH . I 6 HOH A 47 547 2064 HOH HOH . I 6 HOH A 48 548 2024 HOH HOH . I 6 HOH A 49 549 2004 HOH HOH . I 6 HOH A 50 550 2005 HOH HOH . I 6 HOH A 51 551 2061 HOH HOH . I 6 HOH A 52 552 22 HOH HOH . I 6 HOH A 53 553 2031 HOH HOH . I 6 HOH A 54 554 2010 HOH HOH . I 6 HOH A 55 555 24 HOH HOH . I 6 HOH A 56 556 2060 HOH HOH . I 6 HOH A 57 557 17 HOH HOH . I 6 HOH A 58 558 11 HOH HOH . I 6 HOH A 59 559 2 HOH HOH . I 6 HOH A 60 560 23 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 -12.357 24.233 -6.143 1 55.96 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -13.017 24.166 -7.5 1 59.46 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -11.873 22.895 -5.633 1 61.9 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -13.098 25.066 -5.123 1 47.18 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -10.988 26.502 -7.115 1 45.94 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -10.774 26.35 -8.602 1 53.12 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -12.16 27.293 -6.584 1 49.71 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -10.997 25.055 -6.406 1 52.78 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.656 27.114 -6.452 1 43.22 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.477 26.978 -5.044 1 40.98 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.622 28.113 -4.499 1 41.68 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -7.37 28.189 -5.186 1 41.59 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -9.296 29.461 -4.686 1 44.46 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.066 29.817 -3.534 1 48.58 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -8.137 30.41 -4.891 1 46.2 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -7.727 30.916 -3.619 1 45.25 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -7.022 29.549 -5.457 1 39.79 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -6.977 29.74 -6.927 1 45.34 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.669 29.007 -7.819 1 49.36 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.426 29.417 -9.089 1 49.22 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.556 30.44 -9.02 1 43.98 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -5.883 31.33 -9.996 1 46.54 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -6.102 31.199 -11.327 1 49.43 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -5.047 32.275 -9.512 1 44.73 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.825 32.411 -8.19 1 54.59 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -5.401 31.639 -7.25 1 52.24 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.263 30.651 -7.594 1 46.64 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #