data_2OL1 # _model_server_result.job_id tgSt4tywyHQtEMbbsKywdQ _model_server_result.datetime_utc '2025-04-02 01:43:19' _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 2ol1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1201}' # _entry.id 2OL1 # _exptl.entry_id 2OL1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 2OL1 _cell.length_a 119.97 _cell.length_b 119.97 _cell.length_c 50.13 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OL1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 G N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 318 n n N1 C6 UMP sing 319 n n N1 C1' UMP sing 320 n n C2 N3 UMP sing 321 n n C2 O2 UMP doub 322 n n N3 C4 UMP sing 323 n n N3 HN3 UMP sing 324 n n C4 C5 UMP sing 325 n n C4 O4 UMP doub 326 n n C5 C6 UMP doub 327 n n C5 H5 UMP sing 328 n n C6 H6 UMP sing 329 n n C1' C2' UMP sing 330 n n C1' O4' UMP sing 331 n n C1' H1' UMP sing 332 n n C2' C3' UMP sing 333 n n C2' H2' UMP sing 334 n n C2' "H2''" UMP sing 335 n n C3' C4' UMP sing 336 n n C3' O3' UMP sing 337 n n C3' H3' UMP sing 338 n n C4' O4' UMP sing 339 n n C4' C5' UMP sing 340 n n C4' H4' UMP sing 341 n n O3' HO3' UMP sing 342 n n C5' O5' UMP sing 343 n n C5' H5' UMP sing 344 n n C5' "H5''" UMP sing 345 n n O5' P UMP sing 346 n n P OP1 UMP doub 347 n n P OP2 UMP sing 348 n n P OP3 UMP sing 349 n n OP2 HOP2 UMP sing 350 n n OP3 HOP3 UMP sing 351 n n # _atom_sites.entry_id 2OL1 _atom_sites.fract_transf_matrix[1][1] 0.008335 _atom_sites.fract_transf_matrix[1][2] 0.004812 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009625 _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] 0.019948 _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 D 2 CL A 1 301 301 CL CL . E 3 UMP C 1 1201 1201 UMP UMP . F 3 UMP C 1 1202 1202 UMP UMP . G 3 UMP C 1 1203 1203 UMP UMP . H 4 EDO C 1 401 401 EDO EDO . I 4 EDO C 1 402 402 EDO EDO . J 5 HOH A 1 302 1 HOH HOH . J 5 HOH A 2 303 3 HOH HOH . J 5 HOH A 3 304 12 HOH HOH . J 5 HOH A 4 305 13 HOH HOH . J 5 HOH A 5 306 16 HOH HOH . J 5 HOH A 6 307 19 HOH HOH . J 5 HOH A 7 308 21 HOH HOH . J 5 HOH A 8 309 24 HOH HOH . J 5 HOH A 9 310 26 HOH HOH . J 5 HOH A 10 311 28 HOH HOH . J 5 HOH A 11 312 32 HOH HOH . J 5 HOH A 12 313 41 HOH HOH . J 5 HOH A 13 314 44 HOH HOH . J 5 HOH A 14 315 45 HOH HOH . J 5 HOH A 15 316 53 HOH HOH . J 5 HOH A 16 317 55 HOH HOH . J 5 HOH A 17 318 57 HOH HOH . J 5 HOH A 18 319 59 HOH HOH . J 5 HOH A 19 320 61 HOH HOH . J 5 HOH A 20 321 62 HOH HOH . J 5 HOH A 21 322 64 HOH HOH . J 5 HOH A 22 323 66 HOH HOH . J 5 HOH A 23 324 68 HOH HOH . J 5 HOH A 24 325 77 HOH HOH . J 5 HOH A 25 326 81 HOH HOH . J 5 HOH A 26 327 83 HOH HOH . J 5 HOH A 27 328 84 HOH HOH . J 5 HOH A 28 329 86 HOH HOH . J 5 HOH A 29 330 89 HOH HOH . J 5 HOH A 30 331 90 HOH HOH . J 5 HOH A 31 332 91 HOH HOH . J 5 HOH A 32 333 94 HOH HOH . J 5 HOH A 33 334 95 HOH HOH . J 5 HOH A 34 335 97 HOH HOH . J 5 HOH A 35 336 108 HOH HOH . J 5 HOH A 36 337 117 HOH HOH . J 5 HOH A 37 338 119 HOH HOH . J 5 HOH A 38 339 120 HOH HOH . J 5 HOH A 39 340 121 HOH HOH . J 5 HOH A 40 341 122 HOH HOH . J 5 HOH A 41 342 123 HOH HOH . J 5 HOH A 42 343 124 HOH HOH . J 5 HOH A 43 344 127 HOH HOH . J 5 HOH A 44 345 147 HOH HOH . J 5 HOH A 45 346 148 HOH HOH . J 5 HOH A 46 347 151 HOH HOH . J 5 HOH A 47 348 162 HOH HOH . J 5 HOH A 48 349 163 HOH HOH . J 5 HOH A 49 350 166 HOH HOH . J 5 HOH A 50 351 171 HOH HOH . J 5 HOH A 51 352 173 HOH HOH . J 5 HOH A 52 353 177 HOH HOH . J 5 HOH A 53 354 178 HOH HOH . J 5 HOH A 54 355 179 HOH HOH . J 5 HOH A 55 356 181 HOH HOH . J 5 HOH A 56 357 182 HOH HOH . J 5 HOH A 57 358 183 HOH HOH . J 5 HOH A 58 359 185 HOH HOH . J 5 HOH A 59 360 186 HOH HOH . J 5 HOH A 60 361 193 HOH HOH . J 5 HOH A 61 362 197 HOH HOH . J 5 HOH A 62 363 198 HOH HOH . J 5 HOH A 63 364 200 HOH HOH . J 5 HOH A 64 365 208 HOH HOH . J 5 HOH A 65 366 209 HOH HOH . J 5 HOH A 66 367 210 HOH HOH . J 5 HOH A 67 368 211 HOH HOH . J 5 HOH A 68 369 216 HOH HOH . J 5 HOH A 69 370 217 HOH HOH . J 5 HOH A 70 371 222 HOH HOH . J 5 HOH A 71 372 223 HOH HOH . J 5 HOH A 72 373 231 HOH HOH . J 5 HOH A 73 374 232 HOH HOH . J 5 HOH A 74 375 235 HOH HOH . J 5 HOH A 75 376 237 HOH HOH . J 5 HOH A 76 377 239 HOH HOH . J 5 HOH A 77 378 246 HOH HOH . J 5 HOH A 78 379 265 HOH HOH . K 5 HOH B 1 148 6 HOH HOH . K 5 HOH B 2 149 7 HOH HOH . K 5 HOH B 3 150 10 HOH HOH . K 5 HOH B 4 151 15 HOH HOH . K 5 HOH B 5 152 20 HOH HOH . K 5 HOH B 6 153 25 HOH HOH . K 5 HOH B 7 154 27 HOH HOH . K 5 HOH B 8 155 29 HOH HOH . K 5 HOH B 9 156 34 HOH HOH . K 5 HOH B 10 157 35 HOH HOH . K 5 HOH B 11 158 36 HOH HOH . K 5 HOH B 12 159 38 HOH HOH . K 5 HOH B 13 160 39 HOH HOH . K 5 HOH B 14 161 49 HOH HOH . K 5 HOH B 15 162 50 HOH HOH . K 5 HOH B 16 163 56 HOH HOH . K 5 HOH B 17 164 60 HOH HOH . K 5 HOH B 18 165 65 HOH HOH . K 5 HOH B 19 166 67 HOH HOH . K 5 HOH B 20 167 71 HOH HOH . K 5 HOH B 21 168 76 HOH HOH . K 5 HOH B 22 169 79 HOH HOH . K 5 HOH B 23 170 80 HOH HOH . K 5 HOH B 24 171 82 HOH HOH . K 5 HOH B 25 172 85 HOH HOH . K 5 HOH B 26 173 87 HOH HOH . K 5 HOH B 27 174 88 HOH HOH . K 5 HOH B 28 175 92 HOH HOH . K 5 HOH B 29 176 93 HOH HOH . K 5 HOH B 30 177 98 HOH HOH . K 5 HOH B 31 178 100 HOH HOH . K 5 HOH B 32 179 104 HOH HOH . K 5 HOH B 33 180 105 HOH HOH . K 5 HOH B 34 181 107 HOH HOH . K 5 HOH B 35 182 109 HOH HOH . K 5 HOH B 36 183 113 HOH HOH . K 5 HOH B 37 184 115 HOH HOH . K 5 HOH B 38 185 116 HOH HOH . K 5 HOH B 39 186 125 HOH HOH . K 5 HOH B 40 187 126 HOH HOH . K 5 HOH B 41 188 129 HOH HOH . K 5 HOH B 42 189 130 HOH HOH . K 5 HOH B 43 190 134 HOH HOH . K 5 HOH B 44 191 135 HOH HOH . K 5 HOH B 45 192 136 HOH HOH . K 5 HOH B 46 193 138 HOH HOH . K 5 HOH B 47 194 142 HOH HOH . K 5 HOH B 48 195 143 HOH HOH . K 5 HOH B 49 196 144 HOH HOH . K 5 HOH B 50 197 149 HOH HOH . K 5 HOH B 51 198 150 HOH HOH . K 5 HOH B 52 199 152 HOH HOH . K 5 HOH B 53 200 155 HOH HOH . K 5 HOH B 54 201 157 HOH HOH . K 5 HOH B 55 202 159 HOH HOH . K 5 HOH B 56 203 160 HOH HOH . K 5 HOH B 57 204 161 HOH HOH . K 5 HOH B 58 205 168 HOH HOH . K 5 HOH B 59 206 172 HOH HOH . K 5 HOH B 60 207 174 HOH HOH . K 5 HOH B 61 208 180 HOH HOH . K 5 HOH B 62 209 184 HOH HOH . K 5 HOH B 63 210 187 HOH HOH . K 5 HOH B 64 211 188 HOH HOH . K 5 HOH B 65 212 189 HOH HOH . K 5 HOH B 66 213 194 HOH HOH . K 5 HOH B 67 214 195 HOH HOH . K 5 HOH B 68 215 201 HOH HOH . K 5 HOH B 69 216 204 HOH HOH . K 5 HOH B 70 217 205 HOH HOH . K 5 HOH B 71 218 207 HOH HOH . K 5 HOH B 72 219 214 HOH HOH . K 5 HOH B 73 220 215 HOH HOH . K 5 HOH B 74 221 233 HOH HOH . K 5 HOH B 75 222 234 HOH HOH . K 5 HOH B 76 223 244 HOH HOH . K 5 HOH B 77 224 250 HOH HOH . K 5 HOH B 78 225 251 HOH HOH . K 5 HOH B 79 226 260 HOH HOH . K 5 HOH B 80 227 261 HOH HOH . K 5 HOH B 81 228 266 HOH HOH . K 5 HOH B 82 229 267 HOH HOH . K 5 HOH B 83 230 268 HOH HOH . K 5 HOH B 84 231 269 HOH HOH . L 5 HOH C 1 1204 2 HOH HOH . L 5 HOH C 2 1205 4 HOH HOH . L 5 HOH C 3 1206 5 HOH HOH . L 5 HOH C 4 1207 8 HOH HOH . L 5 HOH C 5 1208 9 HOH HOH . L 5 HOH C 6 1209 11 HOH HOH . L 5 HOH C 7 1210 14 HOH HOH . L 5 HOH C 8 1211 17 HOH HOH . L 5 HOH C 9 1212 18 HOH HOH . L 5 HOH C 10 1213 22 HOH HOH . L 5 HOH C 11 1214 23 HOH HOH . L 5 HOH C 12 1215 30 HOH HOH . L 5 HOH C 13 1216 31 HOH HOH . L 5 HOH C 14 1217 33 HOH HOH . L 5 HOH C 15 1218 37 HOH HOH . L 5 HOH C 16 1219 40 HOH HOH . L 5 HOH C 17 1220 42 HOH HOH . L 5 HOH C 18 1221 43 HOH HOH . L 5 HOH C 19 1222 46 HOH HOH . L 5 HOH C 20 1223 47 HOH HOH . L 5 HOH C 21 1224 48 HOH HOH . L 5 HOH C 22 1225 51 HOH HOH . L 5 HOH C 23 1226 52 HOH HOH . L 5 HOH C 24 1227 54 HOH HOH . L 5 HOH C 25 1228 58 HOH HOH . L 5 HOH C 26 1229 63 HOH HOH . L 5 HOH C 27 1230 69 HOH HOH . L 5 HOH C 28 1231 70 HOH HOH . L 5 HOH C 29 1232 72 HOH HOH . L 5 HOH C 30 1233 73 HOH HOH . L 5 HOH C 31 1234 74 HOH HOH . L 5 HOH C 32 1235 75 HOH HOH . L 5 HOH C 33 1236 99 HOH HOH . L 5 HOH C 34 1237 101 HOH HOH . L 5 HOH C 35 1238 102 HOH HOH . L 5 HOH C 36 1239 103 HOH HOH . L 5 HOH C 37 1240 106 HOH HOH . L 5 HOH C 38 1241 110 HOH HOH . L 5 HOH C 39 1242 111 HOH HOH . L 5 HOH C 40 1243 112 HOH HOH . L 5 HOH C 41 1244 114 HOH HOH . L 5 HOH C 42 1245 118 HOH HOH . L 5 HOH C 43 1246 128 HOH HOH . L 5 HOH C 44 1247 131 HOH HOH . L 5 HOH C 45 1248 132 HOH HOH . L 5 HOH C 46 1249 133 HOH HOH . L 5 HOH C 47 1250 137 HOH HOH . L 5 HOH C 48 1251 139 HOH HOH . L 5 HOH C 49 1252 140 HOH HOH . L 5 HOH C 50 1253 141 HOH HOH . L 5 HOH C 51 1254 145 HOH HOH . L 5 HOH C 52 1255 153 HOH HOH . L 5 HOH C 53 1256 154 HOH HOH . L 5 HOH C 54 1257 156 HOH HOH . L 5 HOH C 55 1258 164 HOH HOH . L 5 HOH C 56 1259 165 HOH HOH . L 5 HOH C 57 1260 167 HOH HOH . L 5 HOH C 58 1261 169 HOH HOH . L 5 HOH C 59 1262 170 HOH HOH . L 5 HOH C 60 1263 175 HOH HOH . L 5 HOH C 61 1264 176 HOH HOH . L 5 HOH C 62 1265 190 HOH HOH . L 5 HOH C 63 1266 191 HOH HOH . L 5 HOH C 64 1267 196 HOH HOH . L 5 HOH C 65 1268 199 HOH HOH . L 5 HOH C 66 1269 202 HOH HOH . L 5 HOH C 67 1270 203 HOH HOH . L 5 HOH C 68 1271 206 HOH HOH . L 5 HOH C 69 1272 213 HOH HOH . L 5 HOH C 70 1273 218 HOH HOH . L 5 HOH C 71 1274 219 HOH HOH . L 5 HOH C 72 1275 220 HOH HOH . L 5 HOH C 73 1276 221 HOH HOH . L 5 HOH C 74 1277 224 HOH HOH . L 5 HOH C 75 1278 225 HOH HOH . L 5 HOH C 76 1279 226 HOH HOH . L 5 HOH C 77 1280 228 HOH HOH . L 5 HOH C 78 1281 229 HOH HOH . L 5 HOH C 79 1282 230 HOH HOH . L 5 HOH C 80 1283 236 HOH HOH . L 5 HOH C 81 1284 240 HOH HOH . L 5 HOH C 82 1285 241 HOH HOH . L 5 HOH C 83 1286 242 HOH HOH . L 5 HOH C 84 1287 245 HOH HOH . L 5 HOH C 85 1288 247 HOH HOH . L 5 HOH C 86 1289 248 HOH HOH . L 5 HOH C 87 1290 249 HOH HOH . L 5 HOH C 88 1291 252 HOH HOH . L 5 HOH C 89 1292 253 HOH HOH . L 5 HOH C 90 1293 254 HOH HOH . L 5 HOH C 91 1294 256 HOH HOH . L 5 HOH C 92 1295 259 HOH HOH . L 5 HOH C 93 1296 262 HOH HOH . L 5 HOH C 94 1297 263 HOH HOH . L 5 HOH C 95 1298 264 HOH HOH . L 5 HOH C 96 1299 270 HOH HOH . L 5 HOH C 97 1300 271 HOH HOH . L 5 HOH C 98 1301 272 HOH HOH . L 5 HOH C 99 1302 273 HOH HOH . L 5 HOH C 100 1303 274 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 UMP . . . E 3 18.427 28.988 -0.689 1 19.28 ? N1 UMP 1201 C 1 HETATM 2 C C2 UMP . . . E 3 17.581 28.419 -1.63 1 19.64 ? C2 UMP 1201 C 1 HETATM 3 N N3 UMP . . . E 3 16.226 28.718 -1.607 1 19.61 ? N3 UMP 1201 C 1 HETATM 4 C C4 UMP . . . E 3 15.705 29.56 -0.647 1 19.42 ? C4 UMP 1201 C 1 HETATM 5 C C5 UMP . . . E 3 16.548 30.125 0.307 1 19.38 ? C5 UMP 1201 C 1 HETATM 6 C C6 UMP . . . E 3 17.911 29.822 0.273 1 20.14 ? C6 UMP 1201 C 1 HETATM 7 O O2 UMP . . . E 3 18.01 27.666 -2.504 1 19.46 ? O2 UMP 1201 C 1 HETATM 8 O O4 UMP . . . E 3 14.496 29.808 -0.642 1 19.41 ? O4 UMP 1201 C 1 HETATM 9 C C1' UMP . . . E 3 19.877 28.668 -0.704 1 20.06 ? C1' UMP 1201 C 1 HETATM 10 C C2' UMP . . . E 3 20.766 29.912 -0.621 1 20.24 ? C2' UMP 1201 C 1 HETATM 11 C C3' UMP . . . E 3 21.489 29.787 0.708 1 21.19 ? C3' UMP 1201 C 1 HETATM 12 C C4' UMP . . . E 3 21.263 28.351 1.15 1 21.75 ? C4' UMP 1201 C 1 HETATM 13 O O3' UMP . . . E 3 22.872 30.051 0.591 1 22.4 ? O3' UMP 1201 C 1 HETATM 14 O O4' UMP . . . E 3 20.161 27.854 0.415 1 20.37 ? O4' UMP 1201 C 1 HETATM 15 C C5' UMP . . . E 3 20.999 28.237 2.647 1 22.9 ? C5' UMP 1201 C 1 HETATM 16 O O5' UMP . . . E 3 19.925 29.078 3.007 1 25.39 ? O5' UMP 1201 C 1 HETATM 17 P P UMP . . . E 3 19.805 29.668 4.496 1 27 ? P UMP 1201 C 1 HETATM 18 O OP1 UMP . . . E 3 21.146 30.175 4.968 1 27.97 ? OP1 UMP 1201 C 1 HETATM 19 O OP2 UMP . . . E 3 19.35 28.565 5.421 1 27.72 ? OP2 UMP 1201 C 1 HETATM 20 O OP3 UMP . . . E 3 18.82 30.772 4.473 1 26.53 ? OP3 UMP 1201 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #