data_4JX9 # _model_server_result.job_id 1oRoke4C4u8HINAoeAM-Iw _model_server_result.datetime_utc '2024-12-21 13:56:09' _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 4jx9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4JX9 # _exptl.entry_id 4JX9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE _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 4JX9 _cell.length_a 33.945 _cell.length_b 65.783 _cell.length_c 75.752 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JX9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id URI _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE _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 N1 C2 URI sing 345 n n N1 C6 URI sing 346 n n N1 C1' URI sing 347 n n C2 N3 URI sing 348 n n C2 O2 URI doub 349 n n N3 C4 URI sing 350 n n N3 H3 URI sing 351 n n C4 C5 URI sing 352 n n C4 O4 URI doub 353 n n C5 C6 URI doub 354 n n C5 H5 URI sing 355 n n C6 H6 URI sing 356 n n C1' C2' URI sing 357 n n C1' O4' URI sing 358 n n C1' H1' URI sing 359 n n C2' C3' URI sing 360 n n C2' O2' URI sing 361 n n C2' H2' URI sing 362 n n C3' C4' URI sing 363 n n C3' O3' URI sing 364 n n C3' H3' URI sing 365 n n C4' O4' URI sing 366 n n C4' C5' URI sing 367 n n C4' H4' URI sing 368 n n O2' HO2' URI sing 369 n n O3' HO3' URI sing 370 n n C5' O5' URI sing 371 n n C5' "H5'1" URI sing 372 n n C5' "H5'2" URI sing 373 n n O5' HO5' URI sing 374 n n # _atom_sites.entry_id 4JX9 _atom_sites.fract_transf_matrix[1][1] 0.029459 _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] 0.015201 _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] 0.013201 _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 URI A 1 201 1 URI URI . C 3 HOH A 1 301 1 HOH HOH . C 3 HOH A 2 302 2 HOH HOH . C 3 HOH A 3 303 3 HOH HOH . C 3 HOH A 4 304 278 HOH HOH . C 3 HOH A 5 305 279 HOH HOH . C 3 HOH A 6 306 38 HOH HOH . C 3 HOH A 7 307 7 HOH HOH . C 3 HOH A 8 308 8 HOH HOH . C 3 HOH A 9 309 9 HOH HOH . C 3 HOH A 10 310 10 HOH HOH . C 3 HOH A 11 311 11 HOH HOH . C 3 HOH A 12 312 12 HOH HOH . C 3 HOH A 13 313 13 HOH HOH . C 3 HOH A 14 314 14 HOH HOH . C 3 HOH A 15 315 15 HOH HOH . C 3 HOH A 16 316 16 HOH HOH . C 3 HOH A 17 317 17 HOH HOH . C 3 HOH A 18 318 18 HOH HOH . C 3 HOH A 19 319 19 HOH HOH . C 3 HOH A 20 320 20 HOH HOH . C 3 HOH A 21 321 21 HOH HOH . C 3 HOH A 22 322 22 HOH HOH . C 3 HOH A 23 323 23 HOH HOH . C 3 HOH A 24 324 24 HOH HOH . C 3 HOH A 25 325 25 HOH HOH . C 3 HOH A 26 326 26 HOH HOH . C 3 HOH A 27 327 27 HOH HOH . C 3 HOH A 28 328 28 HOH HOH . C 3 HOH A 29 329 29 HOH HOH . C 3 HOH A 30 330 30 HOH HOH . C 3 HOH A 31 331 31 HOH HOH . C 3 HOH A 32 332 32 HOH HOH . C 3 HOH A 33 333 33 HOH HOH . C 3 HOH A 34 334 34 HOH HOH . C 3 HOH A 35 335 35 HOH HOH . C 3 HOH A 36 336 36 HOH HOH . C 3 HOH A 37 337 37 HOH HOH . C 3 HOH A 38 338 6 HOH HOH . C 3 HOH A 39 339 39 HOH HOH . C 3 HOH A 40 340 40 HOH HOH . C 3 HOH A 41 341 41 HOH HOH . C 3 HOH A 42 342 43 HOH HOH . C 3 HOH A 43 343 44 HOH HOH . C 3 HOH A 44 344 45 HOH HOH . C 3 HOH A 45 345 46 HOH HOH . C 3 HOH A 46 346 47 HOH HOH . C 3 HOH A 47 347 48 HOH HOH . C 3 HOH A 48 348 49 HOH HOH . C 3 HOH A 49 349 50 HOH HOH . C 3 HOH A 50 350 51 HOH HOH . C 3 HOH A 51 351 52 HOH HOH . C 3 HOH A 52 352 53 HOH HOH . C 3 HOH A 53 353 54 HOH HOH . C 3 HOH A 54 354 56 HOH HOH . C 3 HOH A 55 355 57 HOH HOH . C 3 HOH A 56 356 58 HOH HOH . C 3 HOH A 57 357 59 HOH HOH . C 3 HOH A 58 358 60 HOH HOH . C 3 HOH A 59 359 61 HOH HOH . C 3 HOH A 60 360 62 HOH HOH . C 3 HOH A 61 361 63 HOH HOH . C 3 HOH A 62 362 64 HOH HOH . C 3 HOH A 63 363 65 HOH HOH . C 3 HOH A 64 364 66 HOH HOH . C 3 HOH A 65 365 67 HOH HOH . C 3 HOH A 66 366 68 HOH HOH . C 3 HOH A 67 367 69 HOH HOH . C 3 HOH A 68 368 70 HOH HOH . C 3 HOH A 69 369 71 HOH HOH . C 3 HOH A 70 370 72 HOH HOH . C 3 HOH A 71 371 75 HOH HOH . C 3 HOH A 72 372 76 HOH HOH . C 3 HOH A 73 373 77 HOH HOH . C 3 HOH A 74 374 78 HOH HOH . C 3 HOH A 75 375 79 HOH HOH . C 3 HOH A 76 376 80 HOH HOH . C 3 HOH A 77 377 81 HOH HOH . C 3 HOH A 78 378 82 HOH HOH . C 3 HOH A 79 379 83 HOH HOH . C 3 HOH A 80 380 87 HOH HOH . C 3 HOH A 81 381 88 HOH HOH . C 3 HOH A 82 382 89 HOH HOH . C 3 HOH A 83 383 90 HOH HOH . C 3 HOH A 84 384 91 HOH HOH . C 3 HOH A 85 385 92 HOH HOH . C 3 HOH A 86 386 93 HOH HOH . C 3 HOH A 87 387 94 HOH HOH . C 3 HOH A 88 388 95 HOH HOH . C 3 HOH A 89 389 96 HOH HOH . C 3 HOH A 90 390 97 HOH HOH . C 3 HOH A 91 391 98 HOH HOH . C 3 HOH A 92 392 100 HOH HOH . C 3 HOH A 93 393 101 HOH HOH . C 3 HOH A 94 394 102 HOH HOH . C 3 HOH A 95 395 103 HOH HOH . C 3 HOH A 96 396 104 HOH HOH . C 3 HOH A 97 397 105 HOH HOH . C 3 HOH A 98 398 107 HOH HOH . C 3 HOH A 99 399 108 HOH HOH . C 3 HOH A 100 400 109 HOH HOH . C 3 HOH A 101 401 110 HOH HOH . C 3 HOH A 102 402 111 HOH HOH . C 3 HOH A 103 403 114 HOH HOH . C 3 HOH A 104 404 115 HOH HOH . C 3 HOH A 105 405 116 HOH HOH . C 3 HOH A 106 406 117 HOH HOH . C 3 HOH A 107 407 119 HOH HOH . C 3 HOH A 108 408 120 HOH HOH . C 3 HOH A 109 409 121 HOH HOH . C 3 HOH A 110 410 122 HOH HOH . C 3 HOH A 111 411 123 HOH HOH . C 3 HOH A 112 412 125 HOH HOH . C 3 HOH A 113 413 126 HOH HOH . C 3 HOH A 114 414 128 HOH HOH . C 3 HOH A 115 415 129 HOH HOH . C 3 HOH A 116 416 130 HOH HOH . C 3 HOH A 117 417 131 HOH HOH . C 3 HOH A 118 418 132 HOH HOH . C 3 HOH A 119 419 133 HOH HOH . C 3 HOH A 120 420 134 HOH HOH . C 3 HOH A 121 421 135 HOH HOH . C 3 HOH A 122 422 136 HOH HOH . C 3 HOH A 123 423 137 HOH HOH . C 3 HOH A 124 424 138 HOH HOH . C 3 HOH A 125 425 139 HOH HOH . C 3 HOH A 126 426 140 HOH HOH . C 3 HOH A 127 427 142 HOH HOH . C 3 HOH A 128 428 143 HOH HOH . C 3 HOH A 129 429 144 HOH HOH . C 3 HOH A 130 430 145 HOH HOH . C 3 HOH A 131 431 146 HOH HOH . C 3 HOH A 132 432 147 HOH HOH . C 3 HOH A 133 433 148 HOH HOH . C 3 HOH A 134 434 150 HOH HOH . C 3 HOH A 135 435 152 HOH HOH . C 3 HOH A 136 436 153 HOH HOH . C 3 HOH A 137 437 154 HOH HOH . C 3 HOH A 138 438 155 HOH HOH . C 3 HOH A 139 439 156 HOH HOH . C 3 HOH A 140 440 158 HOH HOH . C 3 HOH A 141 441 160 HOH HOH . C 3 HOH A 142 442 161 HOH HOH . C 3 HOH A 143 443 162 HOH HOH . C 3 HOH A 144 444 163 HOH HOH . C 3 HOH A 145 445 164 HOH HOH . C 3 HOH A 146 446 165 HOH HOH . C 3 HOH A 147 447 168 HOH HOH . C 3 HOH A 148 448 169 HOH HOH . C 3 HOH A 149 449 170 HOH HOH . C 3 HOH A 150 450 171 HOH HOH . C 3 HOH A 151 451 173 HOH HOH . C 3 HOH A 152 452 176 HOH HOH . C 3 HOH A 153 453 178 HOH HOH . C 3 HOH A 154 454 179 HOH HOH . C 3 HOH A 155 455 180 HOH HOH . C 3 HOH A 156 456 181 HOH HOH . C 3 HOH A 157 457 182 HOH HOH . C 3 HOH A 158 458 185 HOH HOH . C 3 HOH A 159 459 187 HOH HOH . C 3 HOH A 160 460 189 HOH HOH . C 3 HOH A 161 461 193 HOH HOH . C 3 HOH A 162 462 194 HOH HOH . C 3 HOH A 163 463 195 HOH HOH . C 3 HOH A 164 464 198 HOH HOH . C 3 HOH A 165 465 199 HOH HOH . C 3 HOH A 166 466 201 HOH HOH . C 3 HOH A 167 467 202 HOH HOH . C 3 HOH A 168 468 203 HOH HOH . C 3 HOH A 169 469 204 HOH HOH . C 3 HOH A 170 470 205 HOH HOH . C 3 HOH A 171 471 206 HOH HOH . C 3 HOH A 172 472 211 HOH HOH . C 3 HOH A 173 473 214 HOH HOH . C 3 HOH A 174 474 215 HOH HOH . C 3 HOH A 175 475 217 HOH HOH . C 3 HOH A 176 476 220 HOH HOH . C 3 HOH A 177 477 221 HOH HOH . C 3 HOH A 178 478 222 HOH HOH . C 3 HOH A 179 479 225 HOH HOH . C 3 HOH A 180 480 226 HOH HOH . C 3 HOH A 181 481 227 HOH HOH . C 3 HOH A 182 482 228 HOH HOH . C 3 HOH A 183 483 229 HOH HOH . C 3 HOH A 184 484 232 HOH HOH . C 3 HOH A 185 485 234 HOH HOH . C 3 HOH A 186 486 239 HOH HOH . C 3 HOH A 187 487 240 HOH HOH . C 3 HOH A 188 488 241 HOH HOH . C 3 HOH A 189 489 242 HOH HOH . C 3 HOH A 190 490 247 HOH HOH . C 3 HOH A 191 491 249 HOH HOH . C 3 HOH A 192 492 250 HOH HOH . C 3 HOH A 193 493 252 HOH HOH . C 3 HOH A 194 494 253 HOH HOH . C 3 HOH A 195 495 254 HOH HOH . C 3 HOH A 196 496 257 HOH HOH . C 3 HOH A 197 497 258 HOH HOH . C 3 HOH A 198 498 259 HOH HOH . C 3 HOH A 199 499 260 HOH HOH . C 3 HOH A 200 500 261 HOH HOH . C 3 HOH A 201 501 262 HOH HOH . C 3 HOH A 202 502 263 HOH HOH . C 3 HOH A 203 503 264 HOH HOH . C 3 HOH A 204 504 265 HOH HOH . C 3 HOH A 205 505 266 HOH HOH . C 3 HOH A 206 506 267 HOH HOH . C 3 HOH A 207 507 268 HOH HOH . C 3 HOH A 208 508 270 HOH HOH . C 3 HOH A 209 509 271 HOH HOH . C 3 HOH A 210 510 272 HOH HOH . C 3 HOH A 211 511 273 HOH HOH . C 3 HOH A 212 512 274 HOH HOH . C 3 HOH A 213 513 275 HOH HOH . C 3 HOH A 214 514 276 HOH HOH . C 3 HOH A 215 515 277 HOH HOH . C 3 HOH A 216 516 5 HOH HOH . C 3 HOH A 217 517 4 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 URI . . . B 2 2.407 15.901 31.026 1 37.22 ? N1 URI 201 A 1 HETATM 2 C C2 URI . . . B 2 2.806 17.198 31.339 1 38.26 ? C2 URI 201 A 1 HETATM 3 N N3 URI . . . B 2 3.621 17.447 32.328 1 38.92 ? N3 URI 201 A 1 HETATM 4 C C4 URI . . . B 2 4.153 16.444 33.041 1 38.9 ? C4 URI 201 A 1 HETATM 5 C C5 URI . . . B 2 3.785 15.135 32.76 1 38.25 ? C5 URI 201 A 1 HETATM 6 C C6 URI . . . B 2 2.931 14.89 31.683 1 37.65 ? C6 URI 201 A 1 HETATM 7 O O2 URI . . . B 2 2.323 18.157 30.676 1 38.73 ? O2 URI 201 A 1 HETATM 8 O O4 URI . . . B 2 4.953 16.641 34.02 1 39.59 ? O4 URI 201 A 1 HETATM 9 C C1' URI . . . B 2 1.445 15.723 29.906 1 34.87 ? C1' URI 201 A 1 HETATM 10 C C2' URI . . . B 2 2.233 15.305 28.763 1 32.87 ? C2' URI 201 A 1 HETATM 11 C C3' URI . . . B 2 1.884 13.954 28.919 1 31.73 ? C3' URI 201 A 1 HETATM 12 C C4' URI . . . B 2 0.425 13.967 28.788 1 33.24 ? C4' URI 201 A 1 HETATM 13 O O2' URI . . . B 2 1.664 16.117 27.759 1 31.01 ? O2' URI 201 A 1 HETATM 14 O O3' URI . . . B 2 2.568 13.044 28.353 1 31.14 ? O3' URI 201 A 1 HETATM 15 O O4' URI . . . B 2 0.39 14.728 29.963 1 34.78 ? O4' URI 201 A 1 HETATM 16 C C5' URI . . . B 2 -0.081 12.537 28.53 1 33.5 ? C5' URI 201 A 1 HETATM 17 O O5' URI . . . B 2 0.076 12.453 27.101 1 32.61 ? O5' URI 201 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 17 #