data_1IOZ # _model_server_result.job_id NwfhZcH4WciA9AdGgpKdMg _model_server_result.datetime_utc '2024-11-24 01:10:59' _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 1ioz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1180}' # _entry.id 1IOZ # _exptl.entry_id 1IOZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 1IOZ _cell.length_a 82.645 _cell.length_b 82.645 _cell.length_c 102.794 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IOZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 1IOZ _atom_sites.fract_transf_matrix[1][1] 0.0121 _atom_sites.fract_transf_matrix[1][2] 0.006986 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013972 _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] 0.009728 _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 GDP A 1 1180 1180 GDP GDP . C 3 HOH A 1 1181 1 HOH HOH . C 3 HOH A 2 1182 2 HOH HOH . C 3 HOH A 3 1183 3 HOH HOH . C 3 HOH A 4 1184 4 HOH HOH . C 3 HOH A 5 1185 5 HOH HOH . C 3 HOH A 6 1186 6 HOH HOH . C 3 HOH A 7 1187 7 HOH HOH . C 3 HOH A 8 1188 8 HOH HOH . C 3 HOH A 9 1189 9 HOH HOH . C 3 HOH A 10 1190 10 HOH HOH . C 3 HOH A 11 1191 11 HOH HOH . C 3 HOH A 12 1192 12 HOH HOH . C 3 HOH A 13 1193 13 HOH HOH . C 3 HOH A 14 1194 14 HOH HOH . C 3 HOH A 15 1195 15 HOH HOH . C 3 HOH A 16 1196 16 HOH HOH . C 3 HOH A 17 1197 17 HOH HOH . C 3 HOH A 18 1198 18 HOH HOH . C 3 HOH A 19 1199 19 HOH HOH . C 3 HOH A 20 1200 20 HOH HOH . C 3 HOH A 21 1201 21 HOH HOH . C 3 HOH A 22 1202 22 HOH HOH . C 3 HOH A 23 1203 23 HOH HOH . C 3 HOH A 24 1204 24 HOH HOH . C 3 HOH A 25 1205 25 HOH HOH . C 3 HOH A 26 1206 26 HOH HOH . C 3 HOH A 27 1207 27 HOH HOH . C 3 HOH A 28 1208 28 HOH HOH . C 3 HOH A 29 1209 29 HOH HOH . C 3 HOH A 30 1210 30 HOH HOH . C 3 HOH A 31 1211 31 HOH HOH . C 3 HOH A 32 1212 32 HOH HOH . C 3 HOH A 33 1213 33 HOH HOH . C 3 HOH A 34 1214 34 HOH HOH . C 3 HOH A 35 1215 35 HOH HOH . C 3 HOH A 36 1216 36 HOH HOH . C 3 HOH A 37 1217 37 HOH HOH . C 3 HOH A 38 1218 38 HOH HOH . C 3 HOH A 39 1219 39 HOH HOH . C 3 HOH A 40 1220 40 HOH HOH . C 3 HOH A 41 1221 41 HOH HOH . C 3 HOH A 42 1222 42 HOH HOH . C 3 HOH A 43 1223 43 HOH HOH . C 3 HOH A 44 1224 44 HOH HOH . C 3 HOH A 45 1225 45 HOH HOH . C 3 HOH A 46 1226 46 HOH HOH . C 3 HOH A 47 1227 47 HOH HOH . C 3 HOH A 48 1228 48 HOH HOH . C 3 HOH A 49 1229 49 HOH HOH . C 3 HOH A 50 1230 50 HOH HOH . C 3 HOH A 51 1231 51 HOH HOH . C 3 HOH A 52 1232 52 HOH HOH . C 3 HOH A 53 1233 53 HOH HOH . C 3 HOH A 54 1234 54 HOH HOH . C 3 HOH A 55 1235 55 HOH HOH . C 3 HOH A 56 1236 56 HOH HOH . C 3 HOH A 57 1237 57 HOH HOH . C 3 HOH A 58 1238 58 HOH HOH . C 3 HOH A 59 1239 59 HOH HOH . C 3 HOH A 60 1240 60 HOH HOH . C 3 HOH A 61 1241 61 HOH HOH . C 3 HOH A 62 1242 62 HOH HOH . C 3 HOH A 63 1243 63 HOH HOH . C 3 HOH A 64 1244 64 HOH HOH . C 3 HOH A 65 1245 65 HOH HOH . C 3 HOH A 66 1246 66 HOH HOH . C 3 HOH A 67 1247 67 HOH HOH . C 3 HOH A 68 1248 68 HOH HOH . C 3 HOH A 69 1249 69 HOH HOH . C 3 HOH A 70 1250 70 HOH HOH . C 3 HOH A 71 1251 71 HOH HOH . C 3 HOH A 72 1252 72 HOH HOH . C 3 HOH A 73 1253 73 HOH HOH . C 3 HOH A 74 1254 74 HOH HOH . C 3 HOH A 75 1255 75 HOH HOH . C 3 HOH A 76 1256 76 HOH HOH . C 3 HOH A 77 1257 77 HOH HOH . C 3 HOH A 78 1258 78 HOH HOH . C 3 HOH A 79 1259 79 HOH HOH . C 3 HOH A 80 1260 80 HOH HOH . C 3 HOH A 81 1261 81 HOH HOH . C 3 HOH A 82 1262 82 HOH HOH . C 3 HOH A 83 1263 83 HOH HOH . C 3 HOH A 84 1264 84 HOH HOH . C 3 HOH A 85 1265 85 HOH HOH . C 3 HOH A 86 1266 86 HOH HOH . C 3 HOH A 87 1267 87 HOH HOH . C 3 HOH A 88 1268 88 HOH HOH . C 3 HOH A 89 1269 89 HOH HOH . C 3 HOH A 90 1270 90 HOH HOH . C 3 HOH A 91 1271 91 HOH HOH . C 3 HOH A 92 1272 92 HOH HOH . C 3 HOH A 93 1273 93 HOH HOH . C 3 HOH A 94 1274 94 HOH HOH . C 3 HOH A 95 1275 95 HOH HOH . C 3 HOH A 96 1276 96 HOH HOH . C 3 HOH A 97 1277 97 HOH HOH . C 3 HOH A 98 1278 98 HOH HOH . C 3 HOH A 99 1279 99 HOH HOH . C 3 HOH A 100 1280 100 HOH HOH . C 3 HOH A 101 1281 101 HOH HOH . C 3 HOH A 102 1282 102 HOH HOH . C 3 HOH A 103 1283 103 HOH HOH . C 3 HOH A 104 1284 104 HOH HOH . C 3 HOH A 105 1285 105 HOH HOH . C 3 HOH A 106 1286 106 HOH HOH . C 3 HOH A 107 1287 107 HOH HOH . C 3 HOH A 108 1288 108 HOH HOH . C 3 HOH A 109 1289 109 HOH HOH . C 3 HOH A 110 1290 110 HOH HOH . C 3 HOH A 111 1291 111 HOH HOH . C 3 HOH A 112 1292 112 HOH HOH . C 3 HOH A 113 1293 113 HOH HOH . C 3 HOH A 114 1294 114 HOH HOH . C 3 HOH A 115 1295 115 HOH HOH . C 3 HOH A 116 1296 116 HOH HOH . C 3 HOH A 117 1297 117 HOH HOH . C 3 HOH A 118 1298 118 HOH HOH . C 3 HOH A 119 1299 119 HOH HOH . C 3 HOH A 120 1300 120 HOH HOH . C 3 HOH A 121 1301 121 HOH HOH . C 3 HOH A 122 1302 122 HOH HOH . C 3 HOH A 123 1303 123 HOH HOH . C 3 HOH A 124 1304 124 HOH HOH . C 3 HOH A 125 1305 125 HOH HOH . C 3 HOH A 126 1306 126 HOH HOH . C 3 HOH A 127 1307 127 HOH HOH . C 3 HOH A 128 1308 128 HOH HOH . C 3 HOH A 129 1309 129 HOH HOH . C 3 HOH A 130 1310 130 HOH HOH . C 3 HOH A 131 1311 131 HOH HOH . C 3 HOH A 132 1312 132 HOH HOH . C 3 HOH A 133 1313 133 HOH HOH . C 3 HOH A 134 1314 134 HOH HOH . C 3 HOH A 135 1315 135 HOH HOH . C 3 HOH A 136 1316 136 HOH HOH . C 3 HOH A 137 1317 137 HOH HOH . C 3 HOH A 138 1318 138 HOH HOH . C 3 HOH A 139 1319 139 HOH HOH . C 3 HOH A 140 1320 140 HOH HOH . C 3 HOH A 141 1321 141 HOH HOH . C 3 HOH A 142 1322 142 HOH HOH . C 3 HOH A 143 1323 143 HOH HOH . C 3 HOH A 144 1324 144 HOH HOH . C 3 HOH A 145 1325 145 HOH HOH . C 3 HOH A 146 1326 146 HOH HOH . C 3 HOH A 147 1327 147 HOH HOH . C 3 HOH A 148 1328 148 HOH HOH . C 3 HOH A 149 1329 149 HOH HOH . C 3 HOH A 150 1330 150 HOH HOH . C 3 HOH A 151 1331 151 HOH HOH . C 3 HOH A 152 1332 152 HOH HOH . C 3 HOH A 153 1333 153 HOH HOH . C 3 HOH A 154 1334 154 HOH HOH . C 3 HOH A 155 1335 155 HOH HOH . C 3 HOH A 156 1336 156 HOH HOH . C 3 HOH A 157 1337 157 HOH HOH . C 3 HOH A 158 1338 158 HOH HOH . C 3 HOH A 159 1339 159 HOH HOH . C 3 HOH A 160 1340 160 HOH HOH . C 3 HOH A 161 1341 161 HOH HOH . C 3 HOH A 162 1342 162 HOH HOH . C 3 HOH A 163 1343 163 HOH HOH . C 3 HOH A 164 1344 164 HOH HOH . C 3 HOH A 165 1345 165 HOH HOH . C 3 HOH A 166 1346 166 HOH HOH . C 3 HOH A 167 1347 167 HOH HOH . C 3 HOH A 168 1348 168 HOH HOH . C 3 HOH A 169 1349 169 HOH HOH . C 3 HOH A 170 1350 170 HOH HOH . C 3 HOH A 171 1351 171 HOH HOH . C 3 HOH A 172 1352 172 HOH HOH . C 3 HOH A 173 1353 173 HOH HOH . C 3 HOH A 174 1354 174 HOH HOH . C 3 HOH A 175 1355 175 HOH HOH . C 3 HOH A 176 1356 176 HOH HOH . C 3 HOH A 177 1357 177 HOH HOH . C 3 HOH A 178 1358 178 HOH HOH . C 3 HOH A 179 1359 179 HOH HOH . C 3 HOH A 180 1360 180 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 GDP . . . B 2 31.306 11.346 21.573 1 32.81 ? PB GDP 1180 A 1 HETATM 2 O O1B GDP . . . B 2 30.927 12.434 20.564 1 32.78 ? O1B GDP 1180 A 1 HETATM 3 O O2B GDP . . . B 2 32.745 11.226 21.794 1 32.78 ? O2B GDP 1180 A 1 HETATM 4 O O3B GDP . . . B 2 30.744 9.882 21.147 1 32.08 ? O3B GDP 1180 A 1 HETATM 5 O O3A GDP . . . B 2 30.702 11.637 23.011 1 32.36 ? O3A GDP 1180 A 1 HETATM 6 P PA GDP . . . B 2 29.712 10.774 24.042 1 31.65 ? PA GDP 1180 A 1 HETATM 7 O O1A GDP . . . B 2 30.608 9.663 24.607 1 31.78 ? O1A GDP 1180 A 1 HETATM 8 O O2A GDP . . . B 2 28.354 10.4 23.391 1 31.93 ? O2A GDP 1180 A 1 HETATM 9 O O5' GDP . . . B 2 29.544 11.81 25.113 1 33.58 ? O5' GDP 1180 A 1 HETATM 10 C C5' GDP . . . B 2 30.63 12.398 25.809 1 33.59 ? C5' GDP 1180 A 1 HETATM 11 C C4' GDP . . . B 2 30.246 12.883 27.133 1 35.24 ? C4' GDP 1180 A 1 HETATM 12 O O4' GDP . . . B 2 29.219 13.952 27.015 1 32.71 ? O4' GDP 1180 A 1 HETATM 13 C C3' GDP . . . B 2 29.619 11.859 28.072 1 35.56 ? C3' GDP 1180 A 1 HETATM 14 O O3' GDP . . . B 2 30.126 12.02 29.371 1 39.11 ? O3' GDP 1180 A 1 HETATM 15 C C2' GDP . . . B 2 28.136 12.108 27.944 1 36.04 ? C2' GDP 1180 A 1 HETATM 16 O O2' GDP . . . B 2 27.45 11.682 29.14 1 40.09 ? O2' GDP 1180 A 1 HETATM 17 C C1' GDP . . . B 2 28.083 13.642 27.776 1 32.59 ? C1' GDP 1180 A 1 HETATM 18 N N9 GDP . . . B 2 26.901 14.083 27.007 1 31.83 ? N9 GDP 1180 A 1 HETATM 19 C C8 GDP . . . B 2 26.447 13.632 25.773 1 27.14 ? C8 GDP 1180 A 1 HETATM 20 N N7 GDP . . . B 2 25.356 14.243 25.365 1 28.08 ? N7 GDP 1180 A 1 HETATM 21 C C5 GDP . . . B 2 25.058 15.155 26.375 1 28.67 ? C5 GDP 1180 A 1 HETATM 22 C C6 GDP . . . B 2 24.055 16.045 26.49 1 28.9 ? C6 GDP 1180 A 1 HETATM 23 O O6 GDP . . . B 2 23.126 16.253 25.665 1 27.01 ? O6 GDP 1180 A 1 HETATM 24 N N1 GDP . . . B 2 24.077 16.813 27.669 1 28.84 ? N1 GDP 1180 A 1 HETATM 25 C C2 GDP . . . B 2 25.03 16.699 28.656 1 32.34 ? C2 GDP 1180 A 1 HETATM 26 N N2 GDP . . . B 2 24.886 17.543 29.743 1 33.05 ? N2 GDP 1180 A 1 HETATM 27 N N3 GDP . . . B 2 26.076 15.799 28.58 1 30.83 ? N3 GDP 1180 A 1 HETATM 28 C C4 GDP . . . B 2 26.024 15.066 27.416 1 29.17 ? C4 GDP 1180 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #