data_5K9T # _model_server_result.job_id u_Sfv176nvOuojMY187D0w _model_server_result.datetime_utc '2025-03-24 21:31:30' _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 5k9t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 5K9T # _exptl.entry_id 5K9T _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 105.85 _cell.angle_gamma 90 _cell.entry_id 5K9T _cell.length_a 67.065 _cell.length_b 64.45 _cell.length_c 87.967 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K9T _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 metalc ? metalc1 B O1B ADP . A ADP 901 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc2 C MG MG . A MG 902 1_555 D O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc3 C MG MG . A MG 902 1_555 D O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc4 C MG MG . A MG 902 1_555 D O HOH . A HOH 1014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc5 C MG MG . A MG 902 1_555 D O HOH . A HOH 1099 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc6 C MG MG . A MG 902 1_555 D O HOH . A HOH 1116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? # _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 5K9T _atom_sites.fract_transf_matrix[1][1] 0.014911 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004233 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015516 _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] 0.011817 _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 1 901 901 ADP ADP . C 3 MG A 1 902 903 MG MG . D 4 HOH A 1 1001 81 HOH HOH . D 4 HOH A 2 1002 34 HOH HOH . D 4 HOH A 3 1003 163 HOH HOH . D 4 HOH A 4 1004 83 HOH HOH . D 4 HOH A 5 1005 25 HOH HOH . D 4 HOH A 6 1006 145 HOH HOH . D 4 HOH A 7 1007 15 HOH HOH . D 4 HOH A 8 1008 94 HOH HOH . D 4 HOH A 9 1009 92 HOH HOH . D 4 HOH A 10 1010 151 HOH HOH . D 4 HOH A 11 1011 88 HOH HOH . D 4 HOH A 12 1012 143 HOH HOH . D 4 HOH A 13 1013 84 HOH HOH . D 4 HOH A 14 1014 82 HOH HOH . D 4 HOH A 15 1015 11 HOH HOH . D 4 HOH A 16 1016 120 HOH HOH . D 4 HOH A 17 1017 43 HOH HOH . D 4 HOH A 18 1018 68 HOH HOH . D 4 HOH A 19 1019 30 HOH HOH . D 4 HOH A 20 1020 17 HOH HOH . D 4 HOH A 21 1021 112 HOH HOH . D 4 HOH A 22 1022 36 HOH HOH . D 4 HOH A 23 1023 4 HOH HOH . D 4 HOH A 24 1024 121 HOH HOH . D 4 HOH A 25 1025 46 HOH HOH . D 4 HOH A 26 1026 20 HOH HOH . D 4 HOH A 27 1027 6 HOH HOH . D 4 HOH A 28 1028 103 HOH HOH . D 4 HOH A 29 1029 139 HOH HOH . D 4 HOH A 30 1030 45 HOH HOH . D 4 HOH A 31 1031 16 HOH HOH . D 4 HOH A 32 1032 96 HOH HOH . D 4 HOH A 33 1033 52 HOH HOH . D 4 HOH A 34 1034 87 HOH HOH . D 4 HOH A 35 1035 67 HOH HOH . D 4 HOH A 36 1036 99 HOH HOH . D 4 HOH A 37 1037 60 HOH HOH . D 4 HOH A 38 1038 129 HOH HOH . D 4 HOH A 39 1039 108 HOH HOH . D 4 HOH A 40 1040 93 HOH HOH . D 4 HOH A 41 1041 72 HOH HOH . D 4 HOH A 42 1042 86 HOH HOH . D 4 HOH A 43 1043 125 HOH HOH . D 4 HOH A 44 1044 124 HOH HOH . D 4 HOH A 45 1045 42 HOH HOH . D 4 HOH A 46 1046 162 HOH HOH . D 4 HOH A 47 1047 59 HOH HOH . D 4 HOH A 48 1048 12 HOH HOH . D 4 HOH A 49 1049 39 HOH HOH . D 4 HOH A 50 1050 128 HOH HOH . D 4 HOH A 51 1051 90 HOH HOH . D 4 HOH A 52 1052 5 HOH HOH . D 4 HOH A 53 1053 40 HOH HOH . D 4 HOH A 54 1054 65 HOH HOH . D 4 HOH A 55 1055 62 HOH HOH . D 4 HOH A 56 1056 56 HOH HOH . D 4 HOH A 57 1057 69 HOH HOH . D 4 HOH A 58 1058 64 HOH HOH . D 4 HOH A 59 1059 123 HOH HOH . D 4 HOH A 60 1060 111 HOH HOH . D 4 HOH A 61 1061 76 HOH HOH . D 4 HOH A 62 1062 54 HOH HOH . D 4 HOH A 63 1063 10 HOH HOH . D 4 HOH A 64 1064 24 HOH HOH . D 4 HOH A 65 1065 98 HOH HOH . D 4 HOH A 66 1066 118 HOH HOH . D 4 HOH A 67 1067 71 HOH HOH . D 4 HOH A 68 1068 110 HOH HOH . D 4 HOH A 69 1069 61 HOH HOH . D 4 HOH A 70 1070 109 HOH HOH . D 4 HOH A 71 1071 57 HOH HOH . D 4 HOH A 72 1072 50 HOH HOH . D 4 HOH A 73 1073 44 HOH HOH . D 4 HOH A 74 1074 155 HOH HOH . D 4 HOH A 75 1075 13 HOH HOH . D 4 HOH A 76 1076 119 HOH HOH . D 4 HOH A 77 1077 27 HOH HOH . D 4 HOH A 78 1078 136 HOH HOH . D 4 HOH A 79 1079 23 HOH HOH . D 4 HOH A 80 1080 8 HOH HOH . D 4 HOH A 81 1081 29 HOH HOH . D 4 HOH A 82 1082 100 HOH HOH . D 4 HOH A 83 1083 95 HOH HOH . D 4 HOH A 84 1084 85 HOH HOH . D 4 HOH A 85 1085 126 HOH HOH . D 4 HOH A 86 1086 2 HOH HOH . D 4 HOH A 87 1087 58 HOH HOH . D 4 HOH A 88 1088 38 HOH HOH . D 4 HOH A 89 1089 89 HOH HOH . D 4 HOH A 90 1090 113 HOH HOH . D 4 HOH A 91 1091 97 HOH HOH . D 4 HOH A 92 1092 148 HOH HOH . D 4 HOH A 93 1093 47 HOH HOH . D 4 HOH A 94 1094 22 HOH HOH . D 4 HOH A 95 1095 48 HOH HOH . D 4 HOH A 96 1096 104 HOH HOH . D 4 HOH A 97 1097 114 HOH HOH . D 4 HOH A 98 1098 116 HOH HOH . D 4 HOH A 99 1099 1 HOH HOH . D 4 HOH A 100 1100 107 HOH HOH . D 4 HOH A 101 1101 41 HOH HOH . D 4 HOH A 102 1102 122 HOH HOH . D 4 HOH A 103 1103 73 HOH HOH . D 4 HOH A 104 1104 149 HOH HOH . D 4 HOH A 105 1105 28 HOH HOH . D 4 HOH A 106 1106 101 HOH HOH . D 4 HOH A 107 1107 160 HOH HOH . D 4 HOH A 108 1108 130 HOH HOH . D 4 HOH A 109 1109 164 HOH HOH . D 4 HOH A 110 1110 49 HOH HOH . D 4 HOH A 111 1111 159 HOH HOH . D 4 HOH A 112 1112 135 HOH HOH . D 4 HOH A 113 1113 134 HOH HOH . D 4 HOH A 114 1114 32 HOH HOH . D 4 HOH A 115 1115 137 HOH HOH . D 4 HOH A 116 1116 141 HOH HOH . D 4 HOH A 117 1117 140 HOH HOH . D 4 HOH A 118 1118 165 HOH HOH . D 4 HOH A 119 1119 106 HOH HOH . D 4 HOH A 120 1120 166 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 25.413 14.56 10.836 1 21.37 ? PB ADP 901 A 1 HETATM 2 O O1B ADP . . . B 2 24.254 13.768 11.384 1 14.75 ? O1B ADP 901 A 1 HETATM 3 O O2B ADP . . . B 2 26.743 14.009 11.282 1 24 ? O2B ADP 901 A 1 HETATM 4 O O3B ADP . . . B 2 25.34 14.88 9.359 1 19.03 ? O3B ADP 901 A 1 HETATM 5 P PA ADP . . . B 2 24.183 16.554 12.481 1 24.3 ? PA ADP 901 A 1 HETATM 6 O O1A ADP . . . B 2 24.471 15.922 13.822 1 26.5 ? O1A ADP 901 A 1 HETATM 7 O O2A ADP . . . B 2 22.813 16.344 11.87 1 33.3 ? O2A ADP 901 A 1 HETATM 8 O O3A ADP . . . B 2 25.324 16.053 11.454 1 18.49 ? O3A ADP 901 A 1 HETATM 9 O O5' ADP . . . B 2 24.475 18.139 12.559 1 24.67 ? O5' ADP 901 A 1 HETATM 10 C C5' ADP . . . B 2 25.596 18.599 13.325 1 24.09 ? C5' ADP 901 A 1 HETATM 11 C C4' ADP . . . B 2 25.343 20.008 13.827 1 23.85 ? C4' ADP 901 A 1 HETATM 12 O O4' ADP . . . B 2 25.19 20.856 12.699 1 26.8 ? O4' ADP 901 A 1 HETATM 13 C C3' ADP . . . B 2 24.079 20.166 14.658 1 31.77 ? C3' ADP 901 A 1 HETATM 14 O O3' ADP . . . B 2 24.411 20.81 15.886 1 39.97 ? O3' ADP 901 A 1 HETATM 15 C C2' ADP . . . B 2 23.157 21.056 13.85 1 36.53 ? C2' ADP 901 A 1 HETATM 16 O O2' ADP . . . B 2 22.4 21.945 14.681 1 44.83 ? O2' ADP 901 A 1 HETATM 17 C C1' ADP . . . B 2 24.136 21.784 12.943 1 30.42 ? C1' ADP 901 A 1 HETATM 18 N N9 ADP . . . B 2 23.59 22.19 11.629 1 25.2 ? N9 ADP 901 A 1 HETATM 19 C C8 ADP . . . B 2 23.065 21.374 10.7 1 20.52 ? C8 ADP 901 A 1 HETATM 20 N N7 ADP . . . B 2 22.69 22.091 9.615 1 16.45 ? N7 ADP 901 A 1 HETATM 21 C C5 ADP . . . B 2 22.975 23.372 9.852 1 14.76 ? C5 ADP 901 A 1 HETATM 22 C C6 ADP . . . B 2 22.835 24.634 9.122 1 17.35 ? C6 ADP 901 A 1 HETATM 23 N N6 ADP . . . B 2 22.29 24.629 7.892 1 17.41 ? N6 ADP 901 A 1 HETATM 24 N N1 ADP . . . B 2 23.264 25.763 9.72 1 21 ? N1 ADP 901 A 1 HETATM 25 C C2 ADP . . . B 2 23.809 25.759 10.944 1 22.01 ? C2 ADP 901 A 1 HETATM 26 N N3 ADP . . . B 2 23.97 24.636 11.66 1 23.75 ? N3 ADP 901 A 1 HETATM 27 C C4 ADP . . . B 2 23.574 23.439 11.177 1 21.77 ? C4 ADP 901 A 1 HETATM 28 H "H5'1" ADP . . . B 2 26.495 18.586 12.705 1 28.9 ? "H5'1" ADP 901 A 1 HETATM 29 H "H5'2" ADP . . . B 2 25.76 17.931 14.173 1 28.9 ? "H5'2" ADP 901 A 1 HETATM 30 H H4' ADP . . . B 2 26.205 20.332 14.427 1 28.62 ? H4' ADP 901 A 1 HETATM 31 H H3' ADP . . . B 2 23.611 19.187 14.83 1 38.12 ? H3' ADP 901 A 1 HETATM 32 H HO3' ADP . . . B 2 23.612 20.915 16.421 1 47.97 ? HO3' ADP 901 A 1 HETATM 33 H H2' ADP . . . B 2 22.488 20.432 13.24 1 43.83 ? H2' ADP 901 A 1 HETATM 34 H HO2' ADP . . . B 2 21.842 21.43 15.28 1 53.8 ? HO2' ADP 901 A 1 HETATM 35 H H1' ADP . . . B 2 24.526 22.662 13.475 1 36.5 ? H1' ADP 901 A 1 HETATM 36 H H8 ADP . . . B 2 22.958 20.301 10.804 1 24.63 ? H8 ADP 901 A 1 HETATM 37 H HN61 ADP . . . B 2 22.185 25.495 7.382 1 20.89 ? HN61 ADP 901 A 1 HETATM 38 H HN62 ADP . . . B 2 21.978 23.761 7.481 1 20.89 ? HN62 ADP 901 A 1 HETATM 39 H H2 ADP . . . B 2 24.136 26.699 11.37 1 26.41 ? H2 ADP 901 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 62 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 515 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 39 #