data_4O7V # _model_server_result.job_id e_AYiEUWJWc7ZhTrSqYkZQ _model_server_result.datetime_utc '2024-10-19 21:19:38' _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":"B","auth_seq_id":301}' # _entry.id 4O7V # _exptl.entry_id 4O7V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 UDP sing 447 n n N1 C6 UDP sing 448 n n N1 C1' UDP sing 449 n n C2 N3 UDP sing 450 n n C2 O2 UDP doub 451 n n N3 C4 UDP sing 452 n n N3 HN3 UDP sing 453 n n C4 C5 UDP sing 454 n n C4 O4 UDP doub 455 n n C5 C6 UDP doub 456 n n C5 H5 UDP sing 457 n n C6 H6 UDP sing 458 n n C1' C2' UDP sing 459 n n C1' O4' UDP sing 460 n n C1' H1' UDP sing 461 n n C2' O2' UDP sing 462 n n C2' C3' UDP sing 463 n n C2' H2' UDP sing 464 n n O2' HO2' UDP sing 465 n n C3' C4' UDP sing 466 n n C3' O3' UDP sing 467 n n C3' H3' UDP sing 468 n n C4' O4' UDP sing 469 n n C4' C5' UDP sing 470 n n C4' H4' UDP sing 471 n n O3' HO3' UDP sing 472 n n C5' O5' UDP sing 473 n n C5' "H5'1" UDP sing 474 n n C5' "H5'2" UDP sing 475 n n O5' PA UDP sing 476 n n PA O1A UDP doub 477 n n PA O2A UDP sing 478 n n PA O3A UDP sing 479 n n O2A HOA2 UDP sing 480 n n O3A PB UDP sing 481 n n PB O1B UDP doub 482 n n PB O2B UDP sing 483 n n PB O3B UDP sing 484 n n O2B HOB2 UDP sing 485 n n O3B HOB3 UDP sing 486 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 UDP . A . B 2 15.893 -16.429 -6.121 0.5 25.01 ? N1 UDP 301 A 1 HETATM 2 C C2 UDP . A . B 2 16.628 -16.362 -4.916 0.5 24.95 ? C2 UDP 301 A 1 HETATM 3 N N3 UDP . A . B 2 17.809 -15.736 -4.886 0.5 25.79 ? N3 UDP 301 A 1 HETATM 4 C C4 UDP . A . B 2 18.303 -15.169 -5.994 0.5 26.78 ? C4 UDP 301 A 1 HETATM 5 C C5 UDP . A . B 2 17.603 -15.219 -7.197 0.5 26.64 ? C5 UDP 301 A 1 HETATM 6 C C6 UDP . A . B 2 16.373 -15.869 -7.24 0.5 25.92 ? C6 UDP 301 A 1 HETATM 7 O O2 UDP . A . B 2 16.179 -16.888 -3.876 0.5 23.69 ? O2 UDP 301 A 1 HETATM 8 O O4 UDP . A . B 2 19.406 -14.589 -5.943 0.5 28.49 ? O4 UDP 301 A 1 HETATM 9 C C1' UDP . A . B 2 14.604 -17.116 -6.141 0.5 23.62 ? C1' UDP 301 A 1 HETATM 10 C C2' UDP . A . B 2 13.484 -16.127 -6.407 0.5 22.98 ? C2' UDP 301 A 1 HETATM 11 O O2' UDP . A . B 2 12.865 -15.714 -5.187 0.5 22.95 ? O2' UDP 301 A 1 HETATM 12 C C3' UDP . A . B 2 12.511 -16.93 -7.231 0.5 22.42 ? C3' UDP 301 A 1 HETATM 13 C C4' UDP . A . B 2 13.352 -17.984 -7.936 0.5 22.23 ? C4' UDP 301 A 1 HETATM 14 O O4' UDP . A . B 2 14.578 -18.07 -7.209 0.5 23.04 ? O4' UDP 301 A 1 HETATM 15 O O3' UDP . A . B 2 11.623 -17.6 -6.336 0.5 21.91 ? O3' UDP 301 A 1 HETATM 16 C C5' UDP . A . B 2 13.635 -17.619 -9.389 0.5 21.35 ? C5' UDP 301 A 1 HETATM 17 O O5' UDP . A . B 2 13.95 -16.233 -9.482 0.5 20.71 ? O5' UDP 301 A 1 HETATM 18 P PA UDP . A . B 2 14.151 -15.514 -10.903 0.5 20.28 ? PA UDP 301 A 1 HETATM 19 O O1A UDP . A . B 2 15.129 -16.312 -11.732 0.5 20.75 ? O1A UDP 301 A 1 HETATM 20 O O2A UDP . A . B 2 12.799 -15.218 -11.494 0.5 20.48 ? O2A UDP 301 A 1 HETATM 21 O O3A UDP . A . B 2 14.856 -14.129 -10.476 0.5 20.17 ? O3A UDP 301 A 1 HETATM 22 P PB UDP . A . B 2 14.095 -12.883 -9.784 0.5 20.06 ? PB UDP 301 A 1 HETATM 23 O O1B UDP . A . B 2 15.209 -11.875 -9.665 0.5 20.05 ? O1B UDP 301 A 1 HETATM 24 O O2B UDP . A . B 2 12.985 -12.513 -10.728 0.5 19.64 ? O2B UDP 301 A 1 HETATM 25 O O3B UDP . A . B 2 13.594 -13.388 -8.451 0.5 20.55 ? O3B UDP 301 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #