data_3VTF # _model_server_result.job_id Rsqaxaq41ySn60IMSmxSvA _model_server_result.datetime_utc '2024-11-05 01:20:55' _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 3vtf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 3VTF # _exptl.entry_id 3VTF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 125.8 _cell.angle_gamma 90 _cell.entry_id 3VTF _cell.length_a 117.652 _cell.length_b 76.739 _cell.length_c 75.551 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VTF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 367 n n N1 C6 UPG sing 368 n n N1 C1C UPG sing 369 n n C2 N3 UPG sing 370 n n C2 O2 UPG doub 371 n n N3 C4 UPG sing 372 n n N3 HN3 UPG sing 373 n n C4 C5 UPG sing 374 n n C4 O4 UPG doub 375 n n C5 C6 UPG doub 376 n n C5 H5 UPG sing 377 n n C6 H6 UPG sing 378 n n C1C C2C UPG sing 379 n n C1C O4C UPG sing 380 n n C1C H1C UPG sing 381 n n C2C O2C UPG sing 382 n n C2C C3C UPG sing 383 n n C2C H2C UPG sing 384 n n O2C HO2C UPG sing 385 n n C3C C4C UPG sing 386 n n C3C O3C UPG sing 387 n n C3C H3C UPG sing 388 n n C4C O4C UPG sing 389 n n C4C C5C UPG sing 390 n n C4C H4C UPG sing 391 n n O3C HO3C UPG sing 392 n n C5C O5C UPG sing 393 n n C5C H5C1 UPG sing 394 n n C5C H5C2 UPG sing 395 n n O5C PA UPG sing 396 n n PA O1A UPG doub 397 n n PA O2A UPG sing 398 n n PA O3A UPG sing 399 n n O2A HOA2 UPG sing 400 n n O3A PB UPG sing 401 n n PB O1B UPG doub 402 n n PB O2B UPG sing 403 n n PB O3B UPG sing 404 n n O2B HOB2 UPG sing 405 n n O3B C1' UPG sing 406 n n C1' C2' UPG sing 407 n n C1' O5' UPG sing 408 n n C1' H1' UPG sing 409 n n C2' C3' UPG sing 410 n n C2' O2' UPG sing 411 n n C2' H2' UPG sing 412 n n C3' C4' UPG sing 413 n n C3' O3' UPG sing 414 n n C3' H3' UPG sing 415 n n C4' C5' UPG sing 416 n n C4' O4' UPG sing 417 n n C4' H4' UPG sing 418 n n C5' C6' UPG sing 419 n n C5' O5' UPG sing 420 n n C5' H5' UPG sing 421 n n C6' O6' UPG sing 422 n n C6' "H6'1" UPG sing 423 n n C6' "H6'2" UPG sing 424 n n O2' HO2' UPG sing 425 n n O3' HO3' UPG sing 426 n n O4' HO4' UPG sing 427 n n O6' HO6' UPG sing 428 n n # _atom_sites.entry_id 3VTF _atom_sites.fract_transf_matrix[1][1] 0.0085 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00613 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013031 _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] 0.016319 _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 UPG A 1 1001 1001 UPG UPG . C 3 EDO A 1 1002 2001 EDO EDO . D 4 HOH A 1 1101 1 HOH HOH . D 4 HOH A 2 1102 2 HOH HOH . D 4 HOH A 3 1103 3 HOH HOH . D 4 HOH A 4 1104 4 HOH HOH . D 4 HOH A 5 1105 5 HOH HOH . D 4 HOH A 6 1106 6 HOH HOH . D 4 HOH A 7 1107 7 HOH HOH . D 4 HOH A 8 1108 8 HOH HOH . D 4 HOH A 9 1109 9 HOH HOH . D 4 HOH A 10 1110 10 HOH HOH . D 4 HOH A 11 1111 11 HOH HOH . D 4 HOH A 12 1112 12 HOH HOH . D 4 HOH A 13 1113 13 HOH HOH . D 4 HOH A 14 1114 14 HOH HOH . D 4 HOH A 15 1115 15 HOH HOH . D 4 HOH A 16 1116 16 HOH HOH . D 4 HOH A 17 1117 17 HOH HOH . D 4 HOH A 18 1118 18 HOH HOH . D 4 HOH A 19 1119 19 HOH HOH . D 4 HOH A 20 1120 20 HOH HOH . D 4 HOH A 21 1121 21 HOH HOH . D 4 HOH A 22 1122 22 HOH HOH . D 4 HOH A 23 1123 23 HOH HOH . D 4 HOH A 24 1124 24 HOH HOH . D 4 HOH A 25 1125 25 HOH HOH . D 4 HOH A 26 1126 26 HOH HOH . D 4 HOH A 27 1127 27 HOH HOH . D 4 HOH A 28 1128 28 HOH HOH . D 4 HOH A 29 1129 29 HOH HOH . D 4 HOH A 30 1130 30 HOH HOH . D 4 HOH A 31 1131 31 HOH HOH . D 4 HOH A 32 1132 32 HOH HOH . D 4 HOH A 33 1133 33 HOH HOH . D 4 HOH A 34 1134 34 HOH HOH . D 4 HOH A 35 1135 35 HOH HOH . D 4 HOH A 36 1136 36 HOH HOH . D 4 HOH A 37 1137 37 HOH HOH . D 4 HOH A 38 1138 38 HOH HOH . D 4 HOH A 39 1139 39 HOH HOH . D 4 HOH A 40 1140 40 HOH HOH . D 4 HOH A 41 1141 41 HOH HOH . D 4 HOH A 42 1142 42 HOH HOH . D 4 HOH A 43 1143 43 HOH HOH . D 4 HOH A 44 1144 44 HOH HOH . D 4 HOH A 45 1145 45 HOH HOH . D 4 HOH A 46 1146 46 HOH HOH . D 4 HOH A 47 1147 47 HOH HOH . D 4 HOH A 48 1148 48 HOH HOH . D 4 HOH A 49 1149 49 HOH HOH . D 4 HOH A 50 1150 50 HOH HOH . D 4 HOH A 51 1151 51 HOH HOH . D 4 HOH A 52 1152 52 HOH HOH . D 4 HOH A 53 1153 53 HOH HOH . D 4 HOH A 54 1154 54 HOH HOH . D 4 HOH A 55 1155 55 HOH HOH . D 4 HOH A 56 1156 56 HOH HOH . D 4 HOH A 57 1157 57 HOH HOH . D 4 HOH A 58 1158 58 HOH HOH . D 4 HOH A 59 1159 59 HOH HOH . D 4 HOH A 60 1160 60 HOH HOH . D 4 HOH A 61 1161 61 HOH HOH . D 4 HOH A 62 1162 62 HOH HOH . D 4 HOH A 63 1163 63 HOH HOH . D 4 HOH A 64 1164 64 HOH HOH . D 4 HOH A 65 1165 65 HOH HOH . D 4 HOH A 66 1166 66 HOH HOH . D 4 HOH A 67 1167 67 HOH HOH . D 4 HOH A 68 1168 68 HOH HOH . D 4 HOH A 69 1169 69 HOH HOH . D 4 HOH A 70 1170 70 HOH HOH . D 4 HOH A 71 1171 71 HOH HOH . D 4 HOH A 72 1172 72 HOH HOH . D 4 HOH A 73 1173 73 HOH HOH . D 4 HOH A 74 1174 74 HOH HOH . D 4 HOH A 75 1175 75 HOH HOH . D 4 HOH A 76 1176 76 HOH HOH . D 4 HOH A 77 1177 77 HOH HOH . D 4 HOH A 78 1178 78 HOH HOH . D 4 HOH A 79 1179 79 HOH HOH . D 4 HOH A 80 1180 80 HOH HOH . D 4 HOH A 81 1181 81 HOH HOH . D 4 HOH A 82 1182 82 HOH HOH . D 4 HOH A 83 1183 83 HOH HOH . D 4 HOH A 84 1184 84 HOH HOH . D 4 HOH A 85 1185 85 HOH HOH . D 4 HOH A 86 1186 86 HOH HOH . D 4 HOH A 87 1187 87 HOH HOH . D 4 HOH A 88 1188 88 HOH HOH . D 4 HOH A 89 1189 89 HOH HOH . D 4 HOH A 90 1190 90 HOH HOH . D 4 HOH A 91 1191 91 HOH HOH . D 4 HOH A 92 1192 92 HOH HOH . D 4 HOH A 93 1193 93 HOH HOH . D 4 HOH A 94 1194 94 HOH HOH . D 4 HOH A 95 1195 95 HOH HOH . D 4 HOH A 96 1196 96 HOH HOH . D 4 HOH A 97 1197 97 HOH HOH . D 4 HOH A 98 1198 98 HOH HOH . D 4 HOH A 99 1199 99 HOH HOH . D 4 HOH A 100 1200 100 HOH HOH . D 4 HOH A 101 1201 101 HOH HOH . D 4 HOH A 102 1202 102 HOH HOH . D 4 HOH A 103 1203 103 HOH HOH . D 4 HOH A 104 1204 104 HOH HOH . D 4 HOH A 105 1205 105 HOH HOH . D 4 HOH A 106 1206 106 HOH HOH . D 4 HOH A 107 1207 107 HOH HOH . D 4 HOH A 108 1208 108 HOH HOH . D 4 HOH A 109 1209 109 HOH HOH . D 4 HOH A 110 1210 110 HOH HOH . D 4 HOH A 111 1211 111 HOH HOH . D 4 HOH A 112 1212 112 HOH HOH . D 4 HOH A 113 1213 113 HOH HOH . D 4 HOH A 114 1214 114 HOH HOH . D 4 HOH A 115 1215 115 HOH HOH . D 4 HOH A 116 1216 116 HOH HOH . D 4 HOH A 117 1217 117 HOH HOH . D 4 HOH A 118 1218 118 HOH HOH . D 4 HOH A 119 1219 119 HOH HOH . D 4 HOH A 120 1220 120 HOH HOH . D 4 HOH A 121 1221 121 HOH HOH . D 4 HOH A 122 1222 122 HOH HOH . D 4 HOH A 123 1223 123 HOH HOH . D 4 HOH A 124 1224 124 HOH HOH . D 4 HOH A 125 1225 125 HOH HOH . D 4 HOH A 126 1226 126 HOH HOH . D 4 HOH A 127 1227 127 HOH HOH . D 4 HOH A 128 1228 128 HOH HOH . D 4 HOH A 129 1229 129 HOH HOH . D 4 HOH A 130 1230 130 HOH HOH . D 4 HOH A 131 1231 131 HOH HOH . D 4 HOH A 132 1232 132 HOH HOH . D 4 HOH A 133 1233 133 HOH HOH . D 4 HOH A 134 1234 134 HOH HOH . D 4 HOH A 135 1235 135 HOH HOH . D 4 HOH A 136 1236 136 HOH HOH . D 4 HOH A 137 1237 137 HOH HOH . D 4 HOH A 138 1238 138 HOH HOH . D 4 HOH A 139 1239 139 HOH HOH . D 4 HOH A 140 1240 140 HOH HOH . D 4 HOH A 141 1241 141 HOH HOH . D 4 HOH A 142 1242 142 HOH HOH . D 4 HOH A 143 1243 143 HOH HOH . D 4 HOH A 144 1244 144 HOH HOH . D 4 HOH A 145 1245 145 HOH HOH . D 4 HOH A 146 1246 146 HOH HOH . D 4 HOH A 147 1247 147 HOH HOH . D 4 HOH A 148 1248 148 HOH HOH . D 4 HOH A 149 1249 149 HOH HOH . D 4 HOH A 150 1250 150 HOH HOH . D 4 HOH A 151 1251 151 HOH HOH . D 4 HOH A 152 1252 152 HOH HOH . D 4 HOH A 153 1253 153 HOH HOH . D 4 HOH A 154 1254 154 HOH HOH . D 4 HOH A 155 1255 155 HOH HOH . D 4 HOH A 156 1256 156 HOH HOH . D 4 HOH A 157 1257 157 HOH HOH . D 4 HOH A 158 1258 158 HOH HOH . D 4 HOH A 159 1259 159 HOH HOH . D 4 HOH A 160 1260 160 HOH HOH . D 4 HOH A 161 1261 161 HOH HOH . D 4 HOH A 162 1262 162 HOH HOH . D 4 HOH A 163 1263 163 HOH HOH . D 4 HOH A 164 1264 164 HOH HOH . D 4 HOH A 165 1265 165 HOH HOH . D 4 HOH A 166 1266 166 HOH HOH . D 4 HOH A 167 1267 167 HOH HOH . D 4 HOH A 168 1268 168 HOH HOH . D 4 HOH A 169 1269 169 HOH HOH . D 4 HOH A 170 1270 170 HOH HOH . D 4 HOH A 171 1271 171 HOH HOH . D 4 HOH A 172 1272 172 HOH HOH . D 4 HOH A 173 1273 173 HOH HOH . D 4 HOH A 174 1274 174 HOH HOH . D 4 HOH A 175 1275 175 HOH HOH . D 4 HOH A 176 1276 176 HOH HOH . D 4 HOH A 177 1277 177 HOH HOH . D 4 HOH A 178 1278 178 HOH HOH . D 4 HOH A 179 1279 179 HOH HOH . D 4 HOH A 180 1280 180 HOH HOH . D 4 HOH A 181 1281 181 HOH HOH . D 4 HOH A 182 1282 182 HOH HOH . D 4 HOH A 183 1283 183 HOH HOH . D 4 HOH A 184 1284 184 HOH HOH . D 4 HOH A 185 1285 185 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 N N1 UPG . . . B 2 13.295 76.162 3.988 1 23.9 ? N1 UPG 1001 A 1 HETATM 2 C C2 UPG . . . B 2 13.279 75.6 2.677 1 23.29 ? C2 UPG 1001 A 1 HETATM 3 N N3 UPG . . . B 2 12.712 76.29 1.685 1 22.31 ? N3 UPG 1001 A 1 HETATM 4 C C4 UPG . . . B 2 12.085 77.498 1.949 1 24.34 ? C4 UPG 1001 A 1 HETATM 5 C C5 UPG . . . B 2 12.052 78.089 3.26 1 23.78 ? C5 UPG 1001 A 1 HETATM 6 C C6 UPG . . . B 2 12.655 77.332 4.285 1 22.9 ? C6 UPG 1001 A 1 HETATM 7 O O2 UPG . . . B 2 13.816 74.475 2.424 1 22.06 ? O2 UPG 1001 A 1 HETATM 8 O O4 UPG . . . B 2 11.509 78.097 0.98 1 22.33 ? O4 UPG 1001 A 1 HETATM 9 C C1C UPG . . . B 2 13.923 75.309 5.024 1 22.68 ? C1C UPG 1001 A 1 HETATM 10 C C2C UPG . . . B 2 14.989 76.095 5.762 1 25.7 ? C2C UPG 1001 A 1 HETATM 11 O O2C UPG . . . B 2 16.271 75.976 5.15 1 23.54 ? O2C UPG 1001 A 1 HETATM 12 C C3C UPG . . . B 2 14.978 75.428 7.155 1 25.06 ? C3C UPG 1001 A 1 HETATM 13 C C4C UPG . . . B 2 13.523 75.002 7.354 1 21.74 ? C4C UPG 1001 A 1 HETATM 14 O O4C UPG . . . B 2 12.919 75.113 6.046 1 23.46 ? O4C UPG 1001 A 1 HETATM 15 O O3C UPG . . . B 2 15.729 74.186 7.092 1 24.6 ? O3C UPG 1001 A 1 HETATM 16 C C5C UPG . . . B 2 12.741 75.912 8.331 1 26.48 ? C5C UPG 1001 A 1 HETATM 17 O O5C UPG . . . B 2 13.087 77.269 8.029 1 26.47 ? O5C UPG 1001 A 1 HETATM 18 P PA UPG . . . B 2 12.417 78.517 8.944 1 30.73 ? PA UPG 1001 A 1 HETATM 19 O O1A UPG . . . B 2 10.864 78.549 8.769 1 25.13 ? O1A UPG 1001 A 1 HETATM 20 O O2A UPG . . . B 2 13.305 79.773 8.755 1 33.07 ? O2A UPG 1001 A 1 HETATM 21 O O3A UPG . . . B 2 12.936 78.046 10.394 1 29.6 ? O3A UPG 1001 A 1 HETATM 22 P PB UPG . . . B 2 12.231 78.065 11.876 1 31.34 ? PB UPG 1001 A 1 HETATM 23 O O1B UPG . . . B 2 13.066 78.961 12.755 1 32.13 ? O1B UPG 1001 A 1 HETATM 24 O O2B UPG . . . B 2 12.313 76.533 12.092 1 33.54 ? O2B UPG 1001 A 1 HETATM 25 O O3B UPG . . . B 2 10.784 78.734 11.836 1 28.67 ? O3B UPG 1001 A 1 HETATM 26 C C1' UPG . . . B 2 9.581 77.908 11.775 1 28.03 ? C1' UPG 1001 A 1 HETATM 27 C C2' UPG . . . B 2 8.458 78.802 11.296 1 26.37 ? C2' UPG 1001 A 1 HETATM 28 C C3' UPG . . . B 2 8.117 79.795 12.433 1 27.25 ? C3' UPG 1001 A 1 HETATM 29 C C4' UPG . . . B 2 7.761 78.964 13.689 1 28.37 ? C4' UPG 1001 A 1 HETATM 30 C C5' UPG . . . B 2 9.062 78.186 14.137 1 27.96 ? C5' UPG 1001 A 1 HETATM 31 C C6' UPG . . . B 2 8.918 77.248 15.356 1 27.79 ? C6' UPG 1001 A 1 HETATM 32 O O2' UPG . . . B 2 9.159 79.5 10.194 1 25.44 ? O2' UPG 1001 A 1 HETATM 33 O O3' UPG . . . B 2 7.014 80.563 11.995 1 25.38 ? O3' UPG 1001 A 1 HETATM 34 O O4' UPG . . . B 2 7.446 79.904 14.739 1 29.95 ? O4' UPG 1001 A 1 HETATM 35 O O5' UPG . . . B 2 9.28 77.278 13.02 1 31.91 ? O5' UPG 1001 A 1 HETATM 36 O O6' UPG . . . B 2 7.56 76.751 15.433 1 23.12 ? O6' UPG 1001 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 215 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #