data_4O7R # _model_server_result.job_id lRpzCDM5M0gJN_w8rzKWDg _model_server_result.datetime_utc '2025-01-02 21:28:55' _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":"C","auth_seq_id":302}' # _entry.id 4O7R # _exptl.entry_id 4O7R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 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 3 _struct_asym.id C _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 403 n n N1 C6 UDP sing 404 n n N1 C1' UDP sing 405 n n C2 N3 UDP sing 406 n n C2 O2 UDP doub 407 n n N3 C4 UDP sing 408 n n N3 HN3 UDP sing 409 n n C4 C5 UDP sing 410 n n C4 O4 UDP doub 411 n n C5 C6 UDP doub 412 n n C5 H5 UDP sing 413 n n C6 H6 UDP sing 414 n n C1' C2' UDP sing 415 n n C1' O4' UDP sing 416 n n C1' H1' UDP sing 417 n n C2' O2' UDP sing 418 n n C2' C3' UDP sing 419 n n C2' H2' UDP sing 420 n n O2' HO2' UDP sing 421 n n C3' C4' UDP sing 422 n n C3' O3' UDP sing 423 n n C3' H3' UDP sing 424 n n C4' O4' UDP sing 425 n n C4' C5' UDP sing 426 n n C4' H4' UDP sing 427 n n O3' HO3' UDP sing 428 n n C5' O5' UDP sing 429 n n C5' "H5'1" UDP sing 430 n n C5' "H5'2" UDP sing 431 n n O5' PA UDP sing 432 n n PA O1A UDP doub 433 n n PA O2A UDP sing 434 n n PA O3A UDP sing 435 n n O2A HOA2 UDP sing 436 n n O3A PB UDP sing 437 n n PB O1B UDP doub 438 n n PB O2B UDP sing 439 n n PB O3B UDP sing 440 n n O2B HOB2 UDP sing 441 n n O3B HOB3 UDP sing 442 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 UDP . . . C 3 4.015 13.02 25.256 0.8 41.56 ? N1 UDP 302 A 1 HETATM 2 C C2 UDP . . . C 3 4.901 12.926 24.152 0.8 39.8 ? C2 UDP 302 A 1 HETATM 3 N N3 UDP . . . C 3 6.107 12.339 24.278 0.8 40.05 ? N3 UDP 302 A 1 HETATM 4 C C4 UDP . . . C 3 6.493 11.814 25.452 0.8 41.89 ? C4 UDP 302 A 1 HETATM 5 C C5 UDP . . . C 3 5.646 11.877 26.566 0.8 39.66 ? C5 UDP 302 A 1 HETATM 6 C C6 UDP . . . C 3 4.4 12.491 26.439 0.8 41.32 ? C6 UDP 302 A 1 HETATM 7 O O2 UDP . . . C 3 4.548 13.394 23.05 0.8 35.83 ? O2 UDP 302 A 1 HETATM 8 O O4 UDP . . . C 3 7.623 11.278 25.54 0.8 43.18 ? O4 UDP 302 A 1 HETATM 9 C C1' UDP . . . C 3 2.703 13.682 25.027 0.8 44.04 ? C1' UDP 302 A 1 HETATM 10 C C2' UDP . . . C 3 1.733 12.682 24.436 0.8 45.43 ? C2' UDP 302 A 1 HETATM 11 O O2' UDP . . . C 3 0.968 13.39 23.461 0.8 46.94 ? O2' UDP 302 A 1 HETATM 12 C C3' UDP . . . C 3 0.873 12.24 25.604 0.8 45.99 ? C3' UDP 302 A 1 HETATM 13 C C4' UDP . . . C 3 0.953 13.39 26.607 0.8 45.27 ? C4' UDP 302 A 1 HETATM 14 O O4' UDP . . . C 3 2.039 14.229 26.175 0.8 44.36 ? O4' UDP 302 A 1 HETATM 15 O O3' UDP . . . C 3 -0.471 11.98 25.186 0.8 43.57 ? O3' UDP 302 A 1 HETATM 16 C C5' UDP . . . C 3 1.252 12.951 28.039 0.8 46.44 ? C5' UDP 302 A 1 HETATM 17 O O5' UDP . . . C 3 0.559 11.783 28.48 0.8 50.64 ? O5' UDP 302 A 1 HETATM 18 P PA UDP . . . C 3 1.296 10.37 28.798 0.8 48.58 ? PA UDP 302 A 1 HETATM 19 O O1A UDP . . . C 3 2.797 10.552 28.756 0.8 48.59 ? O1A UDP 302 A 1 HETATM 20 O O2A UDP . . . C 3 0.65 9.786 30.034 0.8 50.14 ? O2A UDP 302 A 1 HETATM 21 O O3A UDP . . . C 3 0.847 9.478 27.529 0.8 47.95 ? O3A UDP 302 A 1 HETATM 22 P PB UDP . . . C 3 -0.678 9.011 27.23 0.8 48.37 ? PB UDP 302 A 1 HETATM 23 O O1B UDP . . . C 3 -0.504 8.177 25.978 0.8 48.58 ? O1B UDP 302 A 1 HETATM 24 O O2B UDP . . . C 3 -1.118 8.24 28.459 0.8 43.96 ? O2B UDP 302 A 1 HETATM 25 O O3B UDP . . . C 3 -1.464 10.285 26.981 0.8 48.73 ? O3B UDP 302 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 25 #