data_5OO9 # _model_server_result.job_id 8ardfnVx4WsIH3M5f03I1w _model_server_result.datetime_utc '2025-01-25 10:59:25' _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 5oo9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5OO9 # _exptl.entry_id 5OO9 _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 120 _cell.entry_id 5OO9 _cell.length_a 66.604 _cell.length_b 66.604 _cell.length_c 54.257 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OO9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 317 n n N1 C6 URI sing 318 n n N1 C1' URI sing 319 n n C2 N3 URI sing 320 n n C2 O2 URI doub 321 n n N3 C4 URI sing 322 n n N3 H3 URI sing 323 n n C4 C5 URI sing 324 n n C4 O4 URI doub 325 n n C5 C6 URI doub 326 n n C5 H5 URI sing 327 n n C6 H6 URI sing 328 n n C1' C2' URI sing 329 n n C1' O4' URI sing 330 n n C1' H1' URI sing 331 n n C2' C3' URI sing 332 n n C2' O2' URI sing 333 n n C2' H2' URI sing 334 n n C3' C4' URI sing 335 n n C3' O3' URI sing 336 n n C3' H3' URI sing 337 n n C4' O4' URI sing 338 n n C4' C5' URI sing 339 n n C4' H4' URI sing 340 n n O2' HO2' URI sing 341 n n O3' HO3' URI sing 342 n n C5' O5' URI sing 343 n n C5' "H5'1" URI sing 344 n n C5' "H5'2" URI sing 345 n n O5' HO5' URI sing 346 n n # _atom_sites.entry_id 5OO9 _atom_sites.fract_transf_matrix[1][1] 0.015014 _atom_sites.fract_transf_matrix[1][2] 0.008668 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017337 _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] 0.018431 _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 LIG . C 3 HOH A 1 301 28 HOH HOH . C 3 HOH A 2 302 104 HOH HOH . C 3 HOH A 3 303 177 HOH HOH . C 3 HOH A 4 304 172 HOH HOH . C 3 HOH A 5 305 60 HOH HOH . C 3 HOH A 6 306 41 HOH HOH . C 3 HOH A 7 307 156 HOH HOH . C 3 HOH A 8 308 170 HOH HOH . C 3 HOH A 9 309 34 HOH HOH . C 3 HOH A 10 310 129 HOH HOH . C 3 HOH A 11 311 181 HOH HOH . C 3 HOH A 12 312 54 HOH HOH . C 3 HOH A 13 313 25 HOH HOH . C 3 HOH A 14 314 128 HOH HOH . C 3 HOH A 15 315 20 HOH HOH . C 3 HOH A 16 316 94 HOH HOH . C 3 HOH A 17 317 81 HOH HOH . C 3 HOH A 18 318 167 HOH HOH . C 3 HOH A 19 319 67 HOH HOH . C 3 HOH A 20 320 141 HOH HOH . C 3 HOH A 21 321 3 HOH HOH . C 3 HOH A 22 322 99 HOH HOH . C 3 HOH A 23 323 24 HOH HOH . C 3 HOH A 24 324 180 HOH HOH . C 3 HOH A 25 325 164 HOH HOH . C 3 HOH A 26 326 19 HOH HOH . C 3 HOH A 27 327 7 HOH HOH . C 3 HOH A 28 328 140 HOH HOH . C 3 HOH A 29 329 134 HOH HOH . C 3 HOH A 30 330 190 HOH HOH . C 3 HOH A 31 331 17 HOH HOH . C 3 HOH A 32 332 8 HOH HOH . C 3 HOH A 33 333 89 HOH HOH . C 3 HOH A 34 334 73 HOH HOH . C 3 HOH A 35 335 131 HOH HOH . C 3 HOH A 36 336 18 HOH HOH . C 3 HOH A 37 337 10 HOH HOH . C 3 HOH A 38 338 9 HOH HOH . C 3 HOH A 39 339 4 HOH HOH . C 3 HOH A 40 340 32 HOH HOH . C 3 HOH A 41 341 42 HOH HOH . C 3 HOH A 42 342 108 HOH HOH . C 3 HOH A 43 343 102 HOH HOH . C 3 HOH A 44 344 163 HOH HOH . C 3 HOH A 45 345 183 HOH HOH . C 3 HOH A 46 346 26 HOH HOH . C 3 HOH A 47 347 5 HOH HOH . C 3 HOH A 48 348 61 HOH HOH . C 3 HOH A 49 349 21 HOH HOH . C 3 HOH A 50 350 15 HOH HOH . C 3 HOH A 51 351 13 HOH HOH . C 3 HOH A 52 352 43 HOH HOH . C 3 HOH A 53 353 106 HOH HOH . C 3 HOH A 54 354 39 HOH HOH . C 3 HOH A 55 355 189 HOH HOH . C 3 HOH A 56 356 121 HOH HOH . C 3 HOH A 57 357 175 HOH HOH . C 3 HOH A 58 358 11 HOH HOH . C 3 HOH A 59 359 83 HOH HOH . C 3 HOH A 60 360 12 HOH HOH . C 3 HOH A 61 361 165 HOH HOH . C 3 HOH A 62 362 38 HOH HOH . C 3 HOH A 63 363 78 HOH HOH . C 3 HOH A 64 364 47 HOH HOH . C 3 HOH A 65 365 49 HOH HOH . C 3 HOH A 66 366 44 HOH HOH . C 3 HOH A 67 367 109 HOH HOH . C 3 HOH A 68 368 46 HOH HOH . C 3 HOH A 69 369 142 HOH HOH . C 3 HOH A 70 370 1 HOH HOH . C 3 HOH A 71 371 14 HOH HOH . C 3 HOH A 72 372 157 HOH HOH . C 3 HOH A 73 373 101 HOH HOH . C 3 HOH A 74 374 57 HOH HOH . C 3 HOH A 75 375 23 HOH HOH . C 3 HOH A 76 376 76 HOH HOH . C 3 HOH A 77 377 64 HOH HOH . C 3 HOH A 78 378 118 HOH HOH . C 3 HOH A 79 379 124 HOH HOH . C 3 HOH A 80 380 58 HOH HOH . C 3 HOH A 81 381 80 HOH HOH . C 3 HOH A 82 382 115 HOH HOH . C 3 HOH A 83 383 6 HOH HOH . C 3 HOH A 84 384 123 HOH HOH . C 3 HOH A 85 385 84 HOH HOH . C 3 HOH A 86 386 72 HOH HOH . C 3 HOH A 87 387 68 HOH HOH . C 3 HOH A 88 388 92 HOH HOH . C 3 HOH A 89 389 184 HOH HOH . C 3 HOH A 90 390 56 HOH HOH . C 3 HOH A 91 391 114 HOH HOH . C 3 HOH A 92 392 116 HOH HOH . C 3 HOH A 93 393 161 HOH HOH . C 3 HOH A 94 394 69 HOH HOH . C 3 HOH A 95 395 66 HOH HOH . C 3 HOH A 96 396 16 HOH HOH . C 3 HOH A 97 397 133 HOH HOH . C 3 HOH A 98 398 173 HOH HOH . C 3 HOH A 99 399 138 HOH HOH . C 3 HOH A 100 400 74 HOH HOH . C 3 HOH A 101 401 151 HOH HOH . C 3 HOH A 102 402 29 HOH HOH . C 3 HOH A 103 403 127 HOH HOH . C 3 HOH A 104 404 52 HOH HOH . C 3 HOH A 105 405 107 HOH HOH . C 3 HOH A 106 406 30 HOH HOH . C 3 HOH A 107 407 50 HOH HOH . C 3 HOH A 108 408 27 HOH HOH . C 3 HOH A 109 409 179 HOH HOH . C 3 HOH A 110 410 85 HOH HOH . C 3 HOH A 111 411 2 HOH HOH . C 3 HOH A 112 412 65 HOH HOH . C 3 HOH A 113 413 86 HOH HOH . C 3 HOH A 114 414 59 HOH HOH . C 3 HOH A 115 415 62 HOH HOH . C 3 HOH A 116 416 149 HOH HOH . C 3 HOH A 117 417 174 HOH HOH . C 3 HOH A 118 418 31 HOH HOH . C 3 HOH A 119 419 136 HOH HOH . C 3 HOH A 120 420 130 HOH HOH . C 3 HOH A 121 421 36 HOH HOH . C 3 HOH A 122 422 79 HOH HOH . C 3 HOH A 123 423 158 HOH HOH . C 3 HOH A 124 424 148 HOH HOH . C 3 HOH A 125 425 100 HOH HOH . C 3 HOH A 126 426 98 HOH HOH . C 3 HOH A 127 427 146 HOH HOH . C 3 HOH A 128 428 126 HOH HOH . C 3 HOH A 129 429 103 HOH HOH . C 3 HOH A 130 430 187 HOH HOH . C 3 HOH A 131 431 110 HOH HOH . C 3 HOH A 132 432 168 HOH HOH . C 3 HOH A 133 433 117 HOH HOH . C 3 HOH A 134 434 35 HOH HOH . C 3 HOH A 135 435 51 HOH HOH . C 3 HOH A 136 436 113 HOH HOH . C 3 HOH A 137 437 37 HOH HOH . C 3 HOH A 138 438 111 HOH HOH . C 3 HOH A 139 439 105 HOH HOH . C 3 HOH A 140 440 125 HOH HOH . C 3 HOH A 141 441 144 HOH HOH . C 3 HOH A 142 442 91 HOH HOH . C 3 HOH A 143 443 97 HOH HOH . C 3 HOH A 144 444 186 HOH HOH . C 3 HOH A 145 445 137 HOH HOH . C 3 HOH A 146 446 82 HOH HOH . C 3 HOH A 147 447 40 HOH HOH . C 3 HOH A 148 448 143 HOH HOH . C 3 HOH A 149 449 147 HOH HOH . C 3 HOH A 150 450 122 HOH HOH . C 3 HOH A 151 451 112 HOH HOH . C 3 HOH A 152 452 171 HOH HOH . C 3 HOH A 153 453 95 HOH HOH . C 3 HOH A 154 454 145 HOH HOH . C 3 HOH A 155 455 166 HOH HOH . C 3 HOH A 156 456 22 HOH HOH . C 3 HOH A 157 457 90 HOH HOH . C 3 HOH A 158 458 75 HOH HOH . C 3 HOH A 159 459 135 HOH HOH . C 3 HOH A 160 460 153 HOH HOH . C 3 HOH A 161 461 154 HOH HOH . C 3 HOH A 162 462 33 HOH HOH . C 3 HOH A 163 463 178 HOH HOH . C 3 HOH A 164 464 176 HOH HOH . C 3 HOH A 165 465 48 HOH HOH . C 3 HOH A 166 466 93 HOH HOH . C 3 HOH A 167 467 159 HOH HOH . C 3 HOH A 168 468 182 HOH HOH . C 3 HOH A 169 469 45 HOH HOH . C 3 HOH A 170 470 96 HOH HOH . C 3 HOH A 171 471 185 HOH HOH . C 3 HOH A 172 472 53 HOH HOH . C 3 HOH A 173 473 139 HOH HOH . C 3 HOH A 174 474 120 HOH HOH . C 3 HOH A 175 475 152 HOH HOH . C 3 HOH A 176 476 155 HOH HOH . C 3 HOH A 177 477 169 HOH HOH . C 3 HOH A 178 478 77 HOH HOH . C 3 HOH A 179 479 162 HOH HOH . C 3 HOH A 180 480 150 HOH HOH . C 3 HOH A 181 481 119 HOH HOH . C 3 HOH A 182 482 132 HOH HOH . C 3 HOH A 183 483 63 HOH HOH . C 3 HOH A 184 484 55 HOH HOH . C 3 HOH A 185 485 88 HOH HOH . C 3 HOH A 186 486 87 HOH HOH . C 3 HOH A 187 487 70 HOH HOH . C 3 HOH A 188 488 160 HOH HOH . C 3 HOH A 189 489 71 HOH HOH . C 3 HOH A 190 490 188 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 -56.716 68.19 1.459 1 12.95 ? N1 URI 201 A 1 HETATM 2 C C2 URI . . . B 2 -56.994 67.916 0.131 1 13.29 ? C2 URI 201 A 1 HETATM 3 N N3 URI . . . B 2 -57.408 66.637 -0.123 1 13.86 ? N3 URI 201 A 1 HETATM 4 C C4 URI . . . B 2 -57.564 65.616 0.796 1 13.86 ? C4 URI 201 A 1 HETATM 5 C C5 URI . . . B 2 -57.261 65.972 2.149 1 13.45 ? C5 URI 201 A 1 HETATM 6 C C6 URI . . . B 2 -56.855 67.219 2.434 1 13.68 ? C6 URI 201 A 1 HETATM 7 O O2 URI . . . B 2 -56.894 68.748 -0.76 1 13.64 ? O2 URI 201 A 1 HETATM 8 O O4 URI . . . B 2 -57.949 64.504 0.41 1 15.46 ? O4 URI 201 A 1 HETATM 9 C C1' URI . . . B 2 -56.245 69.546 1.805 1 12.11 ? C1' URI 201 A 1 HETATM 10 C C2' URI . . . B 2 -57.274 70.445 2.477 1 11.68 ? C2' URI 201 A 1 HETATM 11 C C3' URI . . . B 2 -56.347 71.526 3.045 1 11.44 ? C3' URI 201 A 1 HETATM 12 C C4' URI . . . B 2 -55.089 70.737 3.424 1 11.9 ? C4' URI 201 A 1 HETATM 13 O O2' URI . . . B 2 -58.243 70.958 1.571 1 10.93 ? O2' URI 201 A 1 HETATM 14 O O3' URI . . . B 2 -55.989 72.486 2.063 1 11.56 ? O3' URI 201 A 1 HETATM 15 O O4' URI . . . B 2 -55.196 69.454 2.752 1 12.44 ? O4' URI 201 A 1 HETATM 16 C C5' URI . . . B 2 -54.906 70.558 4.924 1 12.79 ? C5' URI 201 A 1 HETATM 17 O O5' URI . . . B 2 -53.853 69.693 5.249 1 12.98 ? O5' URI 201 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #