data_5OO8 # _model_server_result.job_id n3bmumI4muIez_bDh5RGTg _model_server_result.datetime_utc '2024-10-19 11:52:31' _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 5oo8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5OO8 # _exptl.entry_id 5OO8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 3 _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 5OO8 _cell.length_a 66.39 _cell.length_b 66.39 _cell.length_c 54.841 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OO8 _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,D _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 3 _struct_asym.id C _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 326 n n N1 C6 URI sing 327 n n N1 C1' URI sing 328 n n C2 N3 URI sing 329 n n C2 O2 URI doub 330 n n N3 C4 URI sing 331 n n N3 H3 URI sing 332 n n C4 C5 URI sing 333 n n C4 O4 URI doub 334 n n C5 C6 URI doub 335 n n C5 H5 URI sing 336 n n C6 H6 URI sing 337 n n C1' C2' URI sing 338 n n C1' O4' URI sing 339 n n C1' H1' URI sing 340 n n C2' C3' URI sing 341 n n C2' O2' URI sing 342 n n C2' H2' URI sing 343 n n C3' C4' URI sing 344 n n C3' O3' URI sing 345 n n C3' H3' URI sing 346 n n C4' O4' URI sing 347 n n C4' C5' URI sing 348 n n C4' H4' URI sing 349 n n O2' HO2' URI sing 350 n n O3' HO3' URI sing 351 n n C5' O5' URI sing 352 n n C5' "H5'1" URI sing 353 n n C5' "H5'2" URI sing 354 n n O5' HO5' URI sing 355 n n # _atom_sites.entry_id 5OO8 _atom_sites.fract_transf_matrix[1][1] 0.015063 _atom_sites.fract_transf_matrix[1][2] 0.008696 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017393 _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] 0.018235 _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 EDO A 1 201 1 EDO EDO . C 3 URI A 1 202 1 URI URI . D 4 HOH A 1 301 126 HOH HOH . D 4 HOH A 2 302 50 HOH HOH . D 4 HOH A 3 303 99 HOH HOH . D 4 HOH A 4 304 136 HOH HOH . D 4 HOH A 5 305 133 HOH HOH . D 4 HOH A 6 306 24 HOH HOH . D 4 HOH A 7 307 123 HOH HOH . D 4 HOH A 8 308 78 HOH HOH . D 4 HOH A 9 309 80 HOH HOH . D 4 HOH A 10 310 4 HOH HOH . D 4 HOH A 11 311 95 HOH HOH . D 4 HOH A 12 312 13 HOH HOH . D 4 HOH A 13 313 105 HOH HOH . D 4 HOH A 14 314 86 HOH HOH . D 4 HOH A 15 315 72 HOH HOH . D 4 HOH A 16 316 18 HOH HOH . D 4 HOH A 17 317 110 HOH HOH . D 4 HOH A 18 318 91 HOH HOH . D 4 HOH A 19 319 129 HOH HOH . D 4 HOH A 20 320 113 HOH HOH . D 4 HOH A 21 321 125 HOH HOH . D 4 HOH A 22 322 102 HOH HOH . D 4 HOH A 23 323 56 HOH HOH . D 4 HOH A 24 324 71 HOH HOH . D 4 HOH A 25 325 34 HOH HOH . D 4 HOH A 26 326 64 HOH HOH . D 4 HOH A 27 327 68 HOH HOH . D 4 HOH A 28 328 130 HOH HOH . D 4 HOH A 29 329 63 HOH HOH . D 4 HOH A 30 330 39 HOH HOH . D 4 HOH A 31 331 41 HOH HOH . D 4 HOH A 32 332 61 HOH HOH . D 4 HOH A 33 333 65 HOH HOH . D 4 HOH A 34 334 48 HOH HOH . D 4 HOH A 35 335 38 HOH HOH . D 4 HOH A 36 336 62 HOH HOH . D 4 HOH A 37 337 122 HOH HOH . D 4 HOH A 38 338 58 HOH HOH . D 4 HOH A 39 339 73 HOH HOH . D 4 HOH A 40 340 57 HOH HOH . D 4 HOH A 41 341 3 HOH HOH . D 4 HOH A 42 342 74 HOH HOH . D 4 HOH A 43 343 2 HOH HOH . D 4 HOH A 44 344 19 HOH HOH . D 4 HOH A 45 345 6 HOH HOH . D 4 HOH A 46 346 60 HOH HOH . D 4 HOH A 47 347 97 HOH HOH . D 4 HOH A 48 348 66 HOH HOH . D 4 HOH A 49 349 54 HOH HOH . D 4 HOH A 50 350 21 HOH HOH . D 4 HOH A 51 351 44 HOH HOH . D 4 HOH A 52 352 100 HOH HOH . D 4 HOH A 53 353 135 HOH HOH . D 4 HOH A 54 354 59 HOH HOH . D 4 HOH A 55 355 131 HOH HOH . D 4 HOH A 56 356 70 HOH HOH . D 4 HOH A 57 357 35 HOH HOH . D 4 HOH A 58 358 69 HOH HOH . D 4 HOH A 59 359 53 HOH HOH . D 4 HOH A 60 360 17 HOH HOH . D 4 HOH A 61 361 111 HOH HOH . D 4 HOH A 62 362 46 HOH HOH . D 4 HOH A 63 363 82 HOH HOH . D 4 HOH A 64 364 104 HOH HOH . D 4 HOH A 65 365 7 HOH HOH . D 4 HOH A 66 366 14 HOH HOH . D 4 HOH A 67 367 89 HOH HOH . D 4 HOH A 68 368 98 HOH HOH . D 4 HOH A 69 369 76 HOH HOH . D 4 HOH A 70 370 116 HOH HOH . D 4 HOH A 71 371 108 HOH HOH . D 4 HOH A 72 372 55 HOH HOH . D 4 HOH A 73 373 96 HOH HOH . D 4 HOH A 74 374 52 HOH HOH . D 4 HOH A 75 375 25 HOH HOH . D 4 HOH A 76 376 101 HOH HOH . D 4 HOH A 77 377 67 HOH HOH . D 4 HOH A 78 378 47 HOH HOH . D 4 HOH A 79 379 103 HOH HOH . D 4 HOH A 80 380 77 HOH HOH . D 4 HOH A 81 381 75 HOH HOH . D 4 HOH A 82 382 134 HOH HOH . D 4 HOH A 83 383 36 HOH HOH . D 4 HOH A 84 384 30 HOH HOH . D 4 HOH A 85 385 124 HOH HOH . D 4 HOH A 86 386 84 HOH HOH . D 4 HOH A 87 387 138 HOH HOH . D 4 HOH A 88 388 115 HOH HOH . D 4 HOH A 89 389 27 HOH HOH . D 4 HOH A 90 390 5 HOH HOH . D 4 HOH A 91 391 45 HOH HOH . D 4 HOH A 92 392 79 HOH HOH . D 4 HOH A 93 393 92 HOH HOH . D 4 HOH A 94 394 16 HOH HOH . D 4 HOH A 95 395 11 HOH HOH . D 4 HOH A 96 396 114 HOH HOH . D 4 HOH A 97 397 90 HOH HOH . D 4 HOH A 98 398 10 HOH HOH . D 4 HOH A 99 399 85 HOH HOH . D 4 HOH A 100 400 33 HOH HOH . D 4 HOH A 101 401 83 HOH HOH . D 4 HOH A 102 402 12 HOH HOH . D 4 HOH A 103 403 28 HOH HOH . D 4 HOH A 104 404 132 HOH HOH . D 4 HOH A 105 405 93 HOH HOH . D 4 HOH A 106 406 31 HOH HOH . D 4 HOH A 107 407 1 HOH HOH . D 4 HOH A 108 408 42 HOH HOH . D 4 HOH A 109 409 81 HOH HOH . D 4 HOH A 110 410 140 HOH HOH . D 4 HOH A 111 411 107 HOH HOH . D 4 HOH A 112 412 40 HOH HOH . D 4 HOH A 113 413 87 HOH HOH . D 4 HOH A 114 414 88 HOH HOH . D 4 HOH A 115 415 109 HOH HOH . D 4 HOH A 116 416 141 HOH HOH . D 4 HOH A 117 417 94 HOH HOH . D 4 HOH A 118 418 127 HOH HOH . D 4 HOH A 119 419 139 HOH HOH . D 4 HOH A 120 420 43 HOH HOH . D 4 HOH A 121 421 119 HOH HOH . D 4 HOH A 122 422 118 HOH HOH . D 4 HOH A 123 423 51 HOH HOH . D 4 HOH A 124 424 15 HOH HOH . D 4 HOH A 125 425 22 HOH HOH . D 4 HOH A 126 426 128 HOH HOH . D 4 HOH A 127 427 137 HOH HOH . D 4 HOH A 128 428 121 HOH HOH . D 4 HOH A 129 429 32 HOH HOH . D 4 HOH A 130 430 120 HOH HOH . D 4 HOH A 131 431 112 HOH HOH . D 4 HOH A 132 432 37 HOH HOH . D 4 HOH A 133 433 29 HOH HOH . D 4 HOH A 134 434 8 HOH HOH . D 4 HOH A 135 435 9 HOH HOH . D 4 HOH A 136 436 49 HOH HOH . D 4 HOH A 137 437 20 HOH HOH . D 4 HOH A 138 438 106 HOH HOH . D 4 HOH A 139 439 117 HOH HOH . D 4 HOH A 140 440 23 HOH HOH . D 4 HOH A 141 441 26 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 . . . C 3 -56.576 67.592 1.216 1 18.92 ? N1 URI 202 A 1 HETATM 2 C C2 URI . . . C 3 -56.875 67.46 -0.127 1 19.94 ? C2 URI 202 A 1 HETATM 3 N N3 URI . . . C 3 -57.355 66.224 -0.497 1 19.65 ? N3 URI 202 A 1 HETATM 4 C C4 URI . . . C 3 -57.562 65.132 0.327 1 20.04 ? C4 URI 202 A 1 HETATM 5 C C5 URI . . . C 3 -57.238 65.347 1.706 1 19.2 ? C5 URI 202 A 1 HETATM 6 C C6 URI . . . C 3 -56.766 66.543 2.1 1 19.53 ? C6 URI 202 A 1 HETATM 7 O O2 URI . . . C 3 -56.725 68.366 -0.936 1 20.68 ? O2 URI 202 A 1 HETATM 8 O O4 URI . . . C 3 -57.999 64.075 -0.153 1 20.85 ? O4 URI 202 A 1 HETATM 9 C C1' URI . . . C 3 -56.069 68.89 1.69 1 18.55 ? C1' URI 202 A 1 HETATM 10 C C2' URI . . . C 3 -57.104 69.707 2.457 1 18.26 ? C2' URI 202 A 1 HETATM 11 C C3' URI . . . C 3 -56.197 70.621 3.291 1 18.56 ? C3' URI 202 A 1 HETATM 12 C C4' URI . . . C 3 -54.955 69.756 3.542 1 17.93 ? C4' URI 202 A 1 HETATM 13 O O2' URI . . . C 3 -57.982 70.395 1.565 1 18.06 ? O2' URI 202 A 1 HETATM 14 O O3' URI . . . C 3 -55.812 71.8 2.587 1 19.22 ? O3' URI 202 A 1 HETATM 15 O O4' URI . . . C 3 -55.025 68.654 2.609 1 18.7 ? O4' URI 202 A 1 HETATM 16 C C5' URI . . . C 3 -54.805 69.207 4.941 1 17.91 ? C5' URI 202 A 1 HETATM 17 O O5' URI . . . C 3 -54.295 70.184 5.831 1 17.1 ? O5' URI 202 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 17 #