data_4O7V # _model_server_result.job_id EcPAciOQ1NbS7vQXWIrQhQ _model_server_result.datetime_utc '2024-10-19 21:37:03' _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 4o7v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 4O7V # _exptl.entry_id 4O7V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _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 4O7V _cell.length_a 44.16 _cell.length_b 155.12 _cell.length_c 78.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O7V _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_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 44.16 0 -39.15 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 412 n n N1 C6 U5P sing 413 n n N1 C1' U5P sing 414 n n C2 N3 U5P sing 415 n n C2 O2 U5P doub 416 n n N3 C4 U5P sing 417 n n N3 HN3 U5P sing 418 n n C4 C5 U5P sing 419 n n C4 O4 U5P doub 420 n n C5 C6 U5P doub 421 n n C5 H5 U5P sing 422 n n C6 H6 U5P sing 423 n n C1' C2' U5P sing 424 n n C1' O4' U5P sing 425 n n C1' H1' U5P sing 426 n n C2' O2' U5P sing 427 n n C2' C3' U5P sing 428 n n C2' H2' U5P sing 429 n n O2' HO2' U5P sing 430 n n C3' C4' U5P sing 431 n n C3' O3' U5P sing 432 n n C3' H3' U5P sing 433 n n C4' O4' U5P sing 434 n n C4' C5' U5P sing 435 n n C4' H4' U5P sing 436 n n O3' HO3' U5P sing 437 n n C5' O5' U5P sing 438 n n C5' "H5'1" U5P sing 439 n n C5' "H5'2" U5P sing 440 n n O5' P U5P sing 441 n n P O1P U5P doub 442 n n P O2P U5P sing 443 n n P O3P U5P sing 444 n n O2P HOP2 U5P sing 445 n n O3P HOP3 U5P sing 446 n n # _atom_sites.entry_id 4O7V _atom_sites.fract_transf_matrix[1][1] 0.022645 _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] 0.006447 _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] 0.012771 _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 UDP A 1 301 420 UDP UDP . C 3 ADP A 1 302 422 ADP ADP . D 4 U5P A 1 303 430 U5P U5P . E 5 ACT A 1 304 502 ACT ACT . F 6 PO4 A 1 305 501 PO4 PO4 . G 7 HOH A 1 401 300 HOH HOH . G 7 HOH A 2 402 301 HOH HOH . G 7 HOH A 3 403 302 HOH HOH . G 7 HOH A 4 404 303 HOH HOH . G 7 HOH A 5 405 304 HOH HOH . G 7 HOH A 6 406 305 HOH HOH . G 7 HOH A 7 407 306 HOH HOH . G 7 HOH A 8 408 307 HOH HOH . G 7 HOH A 9 409 308 HOH HOH . G 7 HOH A 10 410 309 HOH HOH . G 7 HOH A 11 411 310 HOH HOH . G 7 HOH A 12 412 311 HOH HOH . G 7 HOH A 13 413 312 HOH HOH . G 7 HOH A 14 414 313 HOH HOH . G 7 HOH A 15 415 314 HOH HOH . G 7 HOH A 16 416 315 HOH HOH . G 7 HOH A 17 417 316 HOH HOH . G 7 HOH A 18 418 317 HOH HOH . G 7 HOH A 19 419 318 HOH HOH . G 7 HOH A 20 420 319 HOH HOH . G 7 HOH A 21 421 320 HOH HOH . G 7 HOH A 22 422 321 HOH HOH . G 7 HOH A 23 423 322 HOH HOH . G 7 HOH A 24 424 323 HOH HOH . G 7 HOH A 25 425 324 HOH HOH . G 7 HOH A 26 426 325 HOH HOH . G 7 HOH A 27 427 326 HOH HOH . G 7 HOH A 28 428 327 HOH HOH . G 7 HOH A 29 429 328 HOH HOH . G 7 HOH A 30 430 329 HOH HOH . G 7 HOH A 31 431 330 HOH HOH . G 7 HOH A 32 432 331 HOH HOH . G 7 HOH A 33 433 332 HOH HOH . G 7 HOH A 34 434 333 HOH HOH . G 7 HOH A 35 435 334 HOH HOH . G 7 HOH A 36 436 335 HOH HOH . G 7 HOH A 37 437 336 HOH HOH . G 7 HOH A 38 438 337 HOH HOH . G 7 HOH A 39 439 338 HOH HOH . G 7 HOH A 40 440 339 HOH HOH . G 7 HOH A 41 441 340 HOH HOH . G 7 HOH A 42 442 341 HOH HOH . G 7 HOH A 43 443 342 HOH HOH . G 7 HOH A 44 444 343 HOH HOH . G 7 HOH A 45 445 344 HOH HOH . G 7 HOH A 46 446 345 HOH HOH . G 7 HOH A 47 447 346 HOH HOH . G 7 HOH A 48 448 347 HOH HOH . G 7 HOH A 49 449 348 HOH HOH . G 7 HOH A 50 450 349 HOH HOH . G 7 HOH A 51 451 350 HOH HOH . G 7 HOH A 52 452 351 HOH HOH . G 7 HOH A 53 453 352 HOH HOH . G 7 HOH A 54 454 353 HOH HOH . G 7 HOH A 55 455 354 HOH HOH . G 7 HOH A 56 456 355 HOH HOH . G 7 HOH A 57 457 356 HOH HOH . G 7 HOH A 58 458 357 HOH HOH . G 7 HOH A 59 459 358 HOH HOH . G 7 HOH A 60 460 359 HOH HOH . G 7 HOH A 61 461 360 HOH HOH . G 7 HOH A 62 462 361 HOH HOH . G 7 HOH A 63 463 362 HOH HOH . G 7 HOH A 64 464 363 HOH HOH . G 7 HOH A 65 465 364 HOH HOH . G 7 HOH A 66 466 365 HOH HOH . G 7 HOH A 67 467 366 HOH HOH . G 7 HOH A 68 468 367 HOH HOH . G 7 HOH A 69 469 368 HOH HOH . G 7 HOH A 70 470 369 HOH HOH . G 7 HOH A 71 471 370 HOH HOH . G 7 HOH A 72 472 371 HOH HOH . G 7 HOH A 73 473 372 HOH HOH . G 7 HOH A 74 474 373 HOH HOH . G 7 HOH A 75 475 374 HOH HOH . G 7 HOH A 76 476 375 HOH HOH . G 7 HOH A 77 477 376 HOH HOH . G 7 HOH A 78 478 377 HOH HOH . G 7 HOH A 79 479 378 HOH HOH . G 7 HOH A 80 480 379 HOH HOH . G 7 HOH A 81 481 380 HOH HOH . G 7 HOH A 82 482 381 HOH HOH . G 7 HOH A 83 483 382 HOH HOH . G 7 HOH A 84 484 383 HOH HOH . G 7 HOH A 85 485 384 HOH HOH . G 7 HOH A 86 486 385 HOH HOH . G 7 HOH A 87 487 386 HOH HOH . G 7 HOH A 88 488 387 HOH HOH . G 7 HOH A 89 489 388 HOH HOH . G 7 HOH A 90 490 389 HOH HOH . G 7 HOH A 91 491 390 HOH HOH . G 7 HOH A 92 492 391 HOH HOH . G 7 HOH A 93 493 392 HOH HOH . G 7 HOH A 94 494 393 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 . D 4 15.968 -16.639 -6.164 0.5 22.51 ? N1 U5P 303 A 1 HETATM 2 C C2 U5P . B . D 4 16.62 -16.496 -4.917 0.5 22.37 ? C2 U5P 303 A 1 HETATM 3 N N3 U5P . B . D 4 17.854 -15.991 -4.858 0.5 23.02 ? N3 U5P 303 A 1 HETATM 4 C C4 U5P . B . D 4 18.488 -15.625 -5.976 0.5 23.73 ? C4 U5P 303 A 1 HETATM 5 C C5 U5P . B . D 4 17.877 -15.756 -7.222 0.5 23.7 ? C5 U5P 303 A 1 HETATM 6 C C6 U5P . B . D 4 16.59 -16.281 -7.295 0.5 23.13 ? C6 U5P 303 A 1 HETATM 7 O O2 U5P . B . D 4 16.046 -16.838 -3.865 0.5 21.33 ? O2 U5P 303 A 1 HETATM 8 O O4 U5P . B . D 4 19.641 -15.16 -5.891 0.5 25.07 ? O4 U5P 303 A 1 HETATM 9 C C1' U5P . B . D 4 14.619 -17.202 -6.212 0.5 21.42 ? C1' U5P 303 A 1 HETATM 10 C C2' U5P . B . D 4 13.557 -16.145 -6.455 0.5 20.93 ? C2' U5P 303 A 1 HETATM 11 O O2' U5P . B . D 4 12.973 -15.706 -5.227 0.5 20.95 ? O2' U5P 303 A 1 HETATM 12 C C3' U5P . B . D 4 12.529 -16.899 -7.259 0.5 20.49 ? C3' U5P 303 A 1 HETATM 13 C C4' U5P . B . D 4 13.304 -17.979 -7.999 0.5 20.33 ? C4' U5P 303 A 1 HETATM 14 O O3' U5P . B . D 4 11.644 -17.552 -6.348 0.5 20.03 ? O3' U5P 303 A 1 HETATM 15 O O4' U5P . B . D 4 14.542 -18.124 -7.304 0.5 20.99 ? O4' U5P 303 A 1 HETATM 16 C C5' U5P . B . D 4 13.561 -17.614 -9.457 0.5 19.65 ? C5' U5P 303 A 1 HETATM 17 O O5' U5P . B . D 4 14.186 -16.336 -9.528 0.5 19.17 ? O5' U5P 303 A 1 HETATM 18 P P U5P . B . D 4 14.259 -15.515 -10.905 0.5 18.82 ? P U5P 303 A 1 HETATM 19 O O1P U5P . B . D 4 12.856 -15.575 -11.445 0.5 18.86 ? O1P U5P 303 A 1 HETATM 20 O O2P U5P . B . D 4 14.706 -14.144 -10.46 0.5 18.77 ? O2P U5P 303 A 1 HETATM 21 O O3P U5P . B . D 4 15.256 -16.256 -11.764 0.5 19.22 ? O3P U5P 303 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #