data_4O7R # _model_server_result.job_id oZ11hRj40ARN9a5xzlvDuw _model_server_result.datetime_utc '2025-01-02 21:38:09' _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 4o7r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4O7R # _exptl.entry_id 4O7R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 4O7R _cell.length_a 43.8 _cell.length_b 153.07 _cell.length_c 77.69 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O7R _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,E,F,G _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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 43.8 0 38.845 # _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 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 U5P sing 368 n n N1 C6 U5P sing 369 n n N1 C1' U5P sing 370 n n C2 N3 U5P sing 371 n n C2 O2 U5P doub 372 n n N3 C4 U5P sing 373 n n N3 HN3 U5P sing 374 n n C4 C5 U5P sing 375 n n C4 O4 U5P doub 376 n n C5 C6 U5P doub 377 n n C5 H5 U5P sing 378 n n C6 H6 U5P sing 379 n n C1' C2' U5P sing 380 n n C1' O4' U5P sing 381 n n C1' H1' U5P sing 382 n n C2' O2' U5P sing 383 n n C2' C3' U5P sing 384 n n C2' H2' U5P sing 385 n n O2' HO2' U5P sing 386 n n C3' C4' U5P sing 387 n n C3' O3' U5P sing 388 n n C3' H3' U5P sing 389 n n C4' O4' U5P sing 390 n n C4' C5' U5P sing 391 n n C4' H4' U5P sing 392 n n O3' HO3' U5P sing 393 n n C5' O5' U5P sing 394 n n C5' "H5'1" U5P sing 395 n n C5' "H5'2" U5P sing 396 n n O5' P U5P sing 397 n n P O1P U5P doub 398 n n P O2P U5P sing 399 n n P O3P U5P sing 400 n n O2P HOP2 U5P sing 401 n n O3P HOP3 U5P sing 402 n n # _atom_sites.entry_id 4O7R _atom_sites.fract_transf_matrix[1][1] 0.022831 _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] 0.006533 _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] 0.012872 _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 U5P A 1 301 420 U5P U5P . C 3 UDP A 1 302 425 UDP UDP . D 4 PO4 A 1 303 501 PO4 PO4 . E 5 ACT A 1 304 502 ACT ACT . F 4 PO4 A 1 305 503 PO4 PO4 . G 6 HOH A 1 401 301 HOH HOH . G 6 HOH A 2 402 302 HOH HOH . G 6 HOH A 3 403 303 HOH HOH . G 6 HOH A 4 404 304 HOH HOH . G 6 HOH A 5 405 305 HOH HOH . G 6 HOH A 6 406 306 HOH HOH . G 6 HOH A 7 407 307 HOH HOH . G 6 HOH A 8 408 308 HOH HOH . G 6 HOH A 9 409 309 HOH HOH . G 6 HOH A 10 410 310 HOH HOH . G 6 HOH A 11 411 311 HOH HOH . G 6 HOH A 12 412 312 HOH HOH . G 6 HOH A 13 413 313 HOH HOH . G 6 HOH A 14 414 314 HOH HOH . G 6 HOH A 15 415 315 HOH HOH . G 6 HOH A 16 416 316 HOH HOH . G 6 HOH A 17 417 317 HOH HOH . G 6 HOH A 18 418 318 HOH HOH . G 6 HOH A 19 419 319 HOH HOH . G 6 HOH A 20 420 320 HOH HOH . G 6 HOH A 21 421 321 HOH HOH . G 6 HOH A 22 422 322 HOH HOH . G 6 HOH A 23 423 323 HOH HOH . G 6 HOH A 24 424 324 HOH HOH . G 6 HOH A 25 425 325 HOH HOH . G 6 HOH A 26 426 326 HOH HOH . G 6 HOH A 27 427 327 HOH HOH . G 6 HOH A 28 428 328 HOH HOH . G 6 HOH A 29 429 329 HOH HOH . G 6 HOH A 30 430 330 HOH HOH . G 6 HOH A 31 431 331 HOH HOH . G 6 HOH A 32 432 332 HOH HOH . G 6 HOH A 33 433 333 HOH HOH . G 6 HOH A 34 434 336 HOH HOH . G 6 HOH A 35 435 337 HOH HOH . G 6 HOH A 36 436 338 HOH HOH . G 6 HOH A 37 437 339 HOH HOH . G 6 HOH A 38 438 340 HOH HOH . G 6 HOH A 39 439 341 HOH HOH . G 6 HOH A 40 440 342 HOH HOH . G 6 HOH A 41 441 343 HOH HOH . G 6 HOH A 42 442 344 HOH HOH . G 6 HOH A 43 443 345 HOH HOH . G 6 HOH A 44 444 346 HOH HOH . G 6 HOH A 45 445 347 HOH HOH . G 6 HOH A 46 446 348 HOH HOH . G 6 HOH A 47 447 349 HOH HOH . G 6 HOH A 48 448 350 HOH HOH . G 6 HOH A 49 449 351 HOH HOH . G 6 HOH A 50 450 352 HOH HOH . G 6 HOH A 51 451 353 HOH HOH . G 6 HOH A 52 452 354 HOH HOH . G 6 HOH A 53 453 355 HOH HOH . G 6 HOH A 54 454 356 HOH HOH . G 6 HOH A 55 455 357 HOH HOH . G 6 HOH A 56 456 358 HOH HOH . G 6 HOH A 57 457 359 HOH HOH . G 6 HOH A 58 458 360 HOH HOH . G 6 HOH A 59 459 361 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 U5P . . . B 2 15.717 16.127 6.135 1 29.51 ? N1 U5P 301 A 1 HETATM 2 C C2 U5P . . . B 2 16.421 16.097 4.888 1 29.31 ? C2 U5P 301 A 1 HETATM 3 N N3 U5P . . . B 2 17.626 15.498 4.797 1 31.08 ? N3 U5P 301 A 1 HETATM 4 C C4 U5P . . . B 2 18.17 14.911 5.89 1 32.71 ? C4 U5P 301 A 1 HETATM 5 C C5 U5P . . . B 2 17.508 14.929 7.126 1 31.15 ? C5 U5P 301 A 1 HETATM 6 C C6 U5P . . . B 2 16.266 15.55 7.229 1 29.79 ? C6 U5P 301 A 1 HETATM 7 O O2 U5P . . . B 2 15.929 16.624 3.874 1 26.47 ? O2 U5P 301 A 1 HETATM 8 O O4 U5P . . . B 2 19.288 14.355 5.81 1 33.64 ? O4 U5P 301 A 1 HETATM 9 C C1' U5P . . . B 2 14.404 16.785 6.228 1 26.56 ? C1' U5P 301 A 1 HETATM 10 C C2' U5P . . . B 2 13.29 15.784 6.486 1 24.73 ? C2' U5P 301 A 1 HETATM 11 O O2' U5P . . . B 2 12.742 15.263 5.273 1 24.37 ? O2' U5P 301 A 1 HETATM 12 C C3' U5P . . . B 2 12.295 16.633 7.254 1 24.73 ? C3' U5P 301 A 1 HETATM 13 C C4' U5P . . . B 2 13.146 17.616 8.064 1 24.98 ? C4' U5P 301 A 1 HETATM 14 O O3' U5P . . . B 2 11.534 17.399 6.33 1 21.93 ? O3' U5P 301 A 1 HETATM 15 O O4' U5P . . . B 2 14.37 17.72 7.325 1 26.62 ? O4' U5P 301 A 1 HETATM 16 C C5' U5P . . . B 2 13.402 17.177 9.515 1 22.88 ? C5' U5P 301 A 1 HETATM 17 O O5' U5P . . . B 2 14.02 15.889 9.533 1 21.5 ? O5' U5P 301 A 1 HETATM 18 P P U5P . . . B 2 14.19 14.982 10.851 1 20.42 ? P U5P 301 A 1 HETATM 19 O O1P U5P . . . B 2 12.872 14.974 11.548 1 19.8 ? O1P U5P 301 A 1 HETATM 20 O O2P U5P . . . B 2 14.597 13.63 10.289 1 21.46 ? O2P U5P 301 A 1 HETATM 21 O O3P U5P . . . B 2 15.299 15.672 11.62 1 22 ? O3P U5P 301 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #