data_3D8C # _model_server_result.job_id fHtkBxFF_Oh1eL5Vk1tAiA _model_server_result.datetime_utc '2024-11-25 07:30:46' _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 3d8c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1351}' # _entry.id 3D8C # _exptl.entry_id 3D8C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-OXOGLUTARIC ACID' _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 90 _cell.entry_id 3D8C _cell.length_a 86.427 _cell.length_b 86.427 _cell.length_c 148.065 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D8C _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1,2 A,B,C,D,E,F,G,H,I 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 86.427 86.427 74.0325 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 A NE2 HIS 199 A HIS 199 1_555 C ZN ZN . A ZN 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc2 A NE2 HIS 279 A HIS 279 1_555 C ZN ZN . A ZN 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc3 C ZN ZN . A ZN 350 1_555 H O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc4 C ZN ZN . A ZN 350 1_555 F O2 AKG . A AKG 1351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc5 C ZN ZN . A ZN 350 1_555 F O5 AKG . A AKG 1351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? # _chem_comp.formula 'C5 H6 O5' _chem_comp.formula_weight 146.098 _chem_comp.id AKG _chem_comp.mon_nstd_flag . _chem_comp.name '2-OXOGLUTARIC ACID' _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 C1 O1 AKG doub 1 n n C1 O2 AKG sing 2 n n C1 C2 AKG sing 3 n n O2 HO2 AKG sing 4 n n C2 O5 AKG doub 5 n n C2 C3 AKG sing 6 n n C3 C4 AKG sing 7 n n C3 H31 AKG sing 8 n n C3 H32 AKG sing 9 n n C4 C5 AKG sing 10 n n C4 H41 AKG sing 11 n n C4 H42 AKG sing 12 n n C5 O3 AKG doub 13 n n C5 O4 AKG sing 14 n n O4 HO4 AKG sing 15 n n # _atom_sites.entry_id 3D8C _atom_sites.fract_transf_matrix[1][1] 0.01157 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01157 _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] 0.006754 _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 C 3 ZN A 1 350 350 ZN ZN . D 4 SO4 A 1 501 501 SO4 SO4 . E 4 SO4 A 1 502 502 SO4 SO4 . F 5 AKG A 1 1351 1351 AKG AKG . G 6 GOL A 1 2000 2000 GOL GOL . H 7 HOH A 1 1001 1001 HOH HOH . H 7 HOH A 2 1002 1002 HOH HOH . H 7 HOH A 3 1003 1003 HOH HOH . H 7 HOH A 4 1004 1004 HOH HOH . H 7 HOH A 5 1005 1005 HOH HOH . H 7 HOH A 6 1006 1006 HOH HOH . H 7 HOH A 7 1007 1007 HOH HOH . H 7 HOH A 8 1008 1008 HOH HOH . H 7 HOH A 9 1009 1009 HOH HOH . H 7 HOH A 10 1010 1010 HOH HOH . H 7 HOH A 11 1011 1011 HOH HOH . H 7 HOH A 12 1012 1012 HOH HOH . H 7 HOH A 13 1013 1013 HOH HOH . H 7 HOH A 14 1014 1014 HOH HOH . H 7 HOH A 15 1015 1015 HOH HOH . H 7 HOH A 16 1016 1016 HOH HOH . H 7 HOH A 17 1017 1017 HOH HOH . H 7 HOH A 18 1018 1018 HOH HOH . H 7 HOH A 19 1019 1019 HOH HOH . H 7 HOH A 20 1020 1020 HOH HOH . H 7 HOH A 21 1021 1021 HOH HOH . H 7 HOH A 22 1022 1022 HOH HOH . H 7 HOH A 23 1023 1023 HOH HOH . H 7 HOH A 24 1024 1024 HOH HOH . H 7 HOH A 25 1025 1025 HOH HOH . H 7 HOH A 26 1026 1026 HOH HOH . H 7 HOH A 27 1027 1027 HOH HOH . H 7 HOH A 28 1028 1028 HOH HOH . H 7 HOH A 29 1029 1029 HOH HOH . H 7 HOH A 30 1030 1030 HOH HOH . H 7 HOH A 31 1031 1031 HOH HOH . H 7 HOH A 32 1032 1032 HOH HOH . H 7 HOH A 33 1033 1033 HOH HOH . H 7 HOH A 34 1034 1034 HOH HOH . H 7 HOH A 35 1035 1035 HOH HOH . H 7 HOH A 36 1036 1036 HOH HOH . H 7 HOH A 37 1037 1037 HOH HOH . H 7 HOH A 38 1038 1038 HOH HOH . H 7 HOH A 39 1039 1039 HOH HOH . H 7 HOH A 40 1040 1040 HOH HOH . H 7 HOH A 41 1042 1042 HOH HOH . H 7 HOH A 42 1043 1043 HOH HOH . H 7 HOH A 43 1044 1044 HOH HOH . H 7 HOH A 44 1045 1045 HOH HOH . H 7 HOH A 45 1046 1046 HOH HOH . H 7 HOH A 46 1047 1047 HOH HOH . H 7 HOH A 47 1048 1048 HOH HOH . H 7 HOH A 48 1049 1049 HOH HOH . H 7 HOH A 49 1050 1050 HOH HOH . H 7 HOH A 50 1051 1051 HOH HOH . H 7 HOH A 51 1052 1052 HOH HOH . H 7 HOH A 52 1053 1053 HOH HOH . H 7 HOH A 53 1054 1054 HOH HOH . H 7 HOH A 54 1055 1055 HOH HOH . H 7 HOH A 55 1056 1056 HOH HOH . H 7 HOH A 56 1057 1057 HOH HOH . H 7 HOH A 57 1058 1058 HOH HOH . H 7 HOH A 58 1059 1059 HOH HOH . H 7 HOH A 59 1062 1062 HOH HOH . H 7 HOH A 60 1064 1064 HOH HOH . H 7 HOH A 61 1065 1065 HOH HOH . H 7 HOH A 62 1066 1066 HOH HOH . H 7 HOH A 63 1067 1067 HOH HOH . H 7 HOH A 64 1068 1068 HOH HOH . H 7 HOH A 65 1069 1069 HOH HOH . H 7 HOH A 66 1070 1070 HOH HOH . H 7 HOH A 67 1071 1071 HOH HOH . H 7 HOH A 68 1072 1072 HOH HOH . H 7 HOH A 69 1073 1073 HOH HOH . H 7 HOH A 70 1074 1074 HOH HOH . H 7 HOH A 71 1075 1075 HOH HOH . H 7 HOH A 72 1076 1076 HOH HOH . H 7 HOH A 73 1077 1077 HOH HOH . H 7 HOH A 74 1078 1078 HOH HOH . H 7 HOH A 75 1079 1079 HOH HOH . H 7 HOH A 76 1080 1080 HOH HOH . H 7 HOH A 77 1081 1081 HOH HOH . H 7 HOH A 78 1082 1082 HOH HOH . H 7 HOH A 79 1083 1083 HOH HOH . H 7 HOH A 80 1084 1084 HOH HOH . H 7 HOH A 81 1085 1085 HOH HOH . H 7 HOH A 82 1086 1086 HOH HOH . H 7 HOH A 83 1087 1087 HOH HOH . H 7 HOH A 84 1088 1088 HOH HOH . H 7 HOH A 85 1089 1089 HOH HOH . H 7 HOH A 86 1090 1090 HOH HOH . H 7 HOH A 87 1091 1091 HOH HOH . H 7 HOH A 88 1092 1092 HOH HOH . H 7 HOH A 89 1093 1093 HOH HOH . H 7 HOH A 90 1094 1094 HOH HOH . H 7 HOH A 91 1096 1096 HOH HOH . H 7 HOH A 92 1097 1097 HOH HOH . H 7 HOH A 93 1098 1098 HOH HOH . H 7 HOH A 94 1099 1099 HOH HOH . H 7 HOH A 95 1100 1100 HOH HOH . H 7 HOH A 96 1101 1101 HOH HOH . H 7 HOH A 97 1103 1103 HOH HOH . H 7 HOH A 98 1104 1104 HOH HOH . H 7 HOH A 99 1105 1105 HOH HOH . H 7 HOH A 100 1106 1106 HOH HOH . H 7 HOH A 101 1107 1107 HOH HOH . H 7 HOH A 102 1108 1108 HOH HOH . H 7 HOH A 103 1109 1109 HOH HOH . H 7 HOH A 104 1110 1110 HOH HOH . H 7 HOH A 105 1111 1111 HOH HOH . H 7 HOH A 106 1112 1112 HOH HOH . H 7 HOH A 107 1113 1113 HOH HOH . H 7 HOH A 108 1114 1114 HOH HOH . H 7 HOH A 109 1115 1115 HOH HOH . H 7 HOH A 110 1116 1116 HOH HOH . H 7 HOH A 111 1117 1117 HOH HOH . H 7 HOH A 112 1118 1118 HOH HOH . H 7 HOH A 113 1119 1119 HOH HOH . H 7 HOH A 114 1120 1120 HOH HOH . H 7 HOH A 115 1121 1121 HOH HOH . H 7 HOH A 116 1122 1122 HOH HOH . H 7 HOH A 117 1123 1123 HOH HOH . H 7 HOH A 118 1124 1124 HOH HOH . H 7 HOH A 119 1125 1125 HOH HOH . H 7 HOH A 120 1126 1126 HOH HOH . H 7 HOH A 121 1127 1127 HOH HOH . H 7 HOH A 122 1128 1128 HOH HOH . H 7 HOH A 123 1129 1129 HOH HOH . H 7 HOH A 124 1130 1130 HOH HOH . H 7 HOH A 125 1131 1131 HOH HOH . H 7 HOH A 126 1132 1132 HOH HOH . H 7 HOH A 127 1133 1133 HOH HOH . H 7 HOH A 128 1134 1134 HOH HOH . H 7 HOH A 129 1135 1135 HOH HOH . H 7 HOH A 130 1136 1136 HOH HOH . H 7 HOH A 131 1137 1137 HOH HOH . H 7 HOH A 132 1139 1139 HOH HOH . H 7 HOH A 133 1140 1140 HOH HOH . H 7 HOH A 134 1141 1141 HOH HOH . H 7 HOH A 135 1142 1142 HOH HOH . H 7 HOH A 136 1143 1143 HOH HOH . H 7 HOH A 137 1144 1144 HOH HOH . H 7 HOH A 138 1145 1145 HOH HOH . H 7 HOH A 139 1146 1146 HOH HOH . H 7 HOH A 140 1147 1147 HOH HOH . H 7 HOH A 141 1149 1149 HOH HOH . H 7 HOH A 142 1150 1150 HOH HOH . H 7 HOH A 143 1151 1151 HOH HOH . H 7 HOH A 144 1152 1152 HOH HOH . H 7 HOH A 145 1153 1153 HOH HOH . H 7 HOH A 146 1154 1154 HOH HOH . H 7 HOH A 147 1155 1155 HOH HOH . H 7 HOH A 148 1156 1156 HOH HOH . H 7 HOH A 149 1157 1157 HOH HOH . H 7 HOH A 150 1158 1158 HOH HOH . H 7 HOH A 151 1159 1159 HOH HOH . H 7 HOH A 152 1160 1160 HOH HOH . H 7 HOH A 153 1161 1161 HOH HOH . H 7 HOH A 154 1162 1162 HOH HOH . H 7 HOH A 155 1163 1163 HOH HOH . H 7 HOH A 156 1165 1165 HOH HOH . H 7 HOH A 157 1166 1166 HOH HOH . H 7 HOH A 158 1167 1167 HOH HOH . H 7 HOH A 159 1168 1168 HOH HOH . H 7 HOH A 160 1169 1169 HOH HOH . H 7 HOH A 161 1170 1170 HOH HOH . H 7 HOH A 162 1171 1171 HOH HOH . H 7 HOH A 163 1172 1172 HOH HOH . H 7 HOH A 164 1173 1173 HOH HOH . H 7 HOH A 165 1174 1174 HOH HOH . H 7 HOH A 166 1176 1176 HOH HOH . H 7 HOH A 167 1177 1177 HOH HOH . H 7 HOH A 168 1178 1178 HOH HOH . H 7 HOH A 169 1179 1179 HOH HOH . H 7 HOH A 170 1180 1180 HOH HOH . H 7 HOH A 171 1181 1181 HOH HOH . H 7 HOH A 172 1182 1182 HOH HOH . H 7 HOH A 173 1183 1183 HOH HOH . H 7 HOH A 174 1184 1184 HOH HOH . H 7 HOH A 175 1185 1185 HOH HOH . H 7 HOH A 176 1186 1186 HOH HOH . H 7 HOH A 177 1187 1187 HOH HOH . H 7 HOH A 178 1188 1188 HOH HOH . H 7 HOH A 179 1189 1189 HOH HOH . H 7 HOH A 180 1190 1190 HOH HOH . H 7 HOH A 181 1191 1191 HOH HOH . H 7 HOH A 182 1192 1192 HOH HOH . H 7 HOH A 183 1193 1193 HOH HOH . H 7 HOH A 184 1194 1194 HOH HOH . H 7 HOH A 185 1195 1195 HOH HOH . H 7 HOH A 186 1196 1196 HOH HOH . H 7 HOH A 187 1197 1197 HOH HOH . H 7 HOH A 188 1198 1198 HOH HOH . H 7 HOH A 189 1199 1199 HOH HOH . H 7 HOH A 190 1200 1200 HOH HOH . H 7 HOH A 191 1201 1201 HOH HOH . H 7 HOH A 192 1202 1202 HOH HOH . H 7 HOH A 193 1203 1203 HOH HOH . H 7 HOH A 194 1204 1204 HOH HOH . H 7 HOH A 195 1205 1205 HOH HOH . H 7 HOH A 196 1206 1206 HOH HOH . H 7 HOH A 197 1207 1207 HOH HOH . H 7 HOH A 198 1208 1208 HOH HOH . H 7 HOH A 199 1209 1209 HOH HOH . H 7 HOH A 200 1210 1210 HOH HOH . H 7 HOH A 201 1212 1212 HOH HOH . H 7 HOH A 202 1213 1213 HOH HOH . H 7 HOH A 203 1214 1214 HOH HOH . H 7 HOH A 204 1215 1215 HOH HOH . H 7 HOH A 205 1216 1216 HOH HOH . H 7 HOH A 206 1217 1217 HOH HOH . H 7 HOH A 207 1218 1218 HOH HOH . H 7 HOH A 208 1219 1219 HOH HOH . H 7 HOH A 209 1220 1220 HOH HOH . H 7 HOH A 210 1222 1222 HOH HOH . H 7 HOH A 211 1223 1223 HOH HOH . H 7 HOH A 212 1224 1224 HOH HOH . H 7 HOH A 213 1225 1225 HOH HOH . H 7 HOH A 214 1226 1226 HOH HOH . I 7 HOH B 1 1041 1041 HOH HOH . I 7 HOH B 2 1060 1060 HOH HOH . I 7 HOH B 3 1061 1061 HOH HOH . I 7 HOH B 4 1063 1063 HOH HOH . I 7 HOH B 5 1095 1095 HOH HOH . I 7 HOH B 6 1102 1102 HOH HOH . I 7 HOH B 7 1138 1138 HOH HOH . I 7 HOH B 8 1164 1164 HOH HOH . I 7 HOH B 9 1211 1211 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 C C1 AKG . . . F 5 22.468 25.176 27.997 1 45.93 ? C1 AKG 1351 A 1 HETATM 2 O O1 AKG . . . F 5 22.366 24.084 27.45 1 45.86 ? O1 AKG 1351 A 1 HETATM 3 O O2 AKG . . . F 5 23.563 25.737 28.021 1 48.31 ? O2 AKG 1351 A 1 HETATM 4 C C2 AKG . . . F 5 21.26 25.835 28.671 1 48.64 ? C2 AKG 1351 A 1 HETATM 5 O O5 AKG . . . F 5 21.437 26.891 29.275 1 45.51 ? O5 AKG 1351 A 1 HETATM 6 C C3 AKG . . . F 5 19.992 25.264 28.558 1 46.34 ? C3 AKG 1351 A 1 HETATM 7 C C4 AKG . . . F 5 18.961 25.682 29.391 1 43.35 ? C4 AKG 1351 A 1 HETATM 8 C C5 AKG . . . F 5 17.562 25.401 28.831 1 47.29 ? C5 AKG 1351 A 1 HETATM 9 O O3 AKG . . . F 5 16.565 25.856 29.393 1 45.73 ? O3 AKG 1351 A 1 HETATM 10 O O4 AKG . . . F 5 17.388 24.721 27.822 1 44.45 ? O4 AKG 1351 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #