data_3IJZ # _model_server_result.job_id lrdIWmBdB0PBDgtB82cUQA _model_server_result.datetime_utc '2024-11-23 23:41:08' _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 3ijz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":469}' # _entry.id 3IJZ # _exptl.entry_id 3IJZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 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 120 _cell.entry_id 3IJZ _cell.length_a 77.656 _cell.length_b 77.656 _cell.length_c 224.969 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IJZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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' 12_545 x,x-y-1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 38.828 -67.252069 37.494833 # _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 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 394 n n N1 C6 UMP sing 395 n n N1 C1' UMP sing 396 n n C2 N3 UMP sing 397 n n C2 O2 UMP doub 398 n n N3 C4 UMP sing 399 n n N3 HN3 UMP sing 400 n n C4 C5 UMP sing 401 n n C4 O4 UMP doub 402 n n C5 C6 UMP doub 403 n n C5 H5 UMP sing 404 n n C6 H6 UMP sing 405 n n C1' C2' UMP sing 406 n n C1' O4' UMP sing 407 n n C1' H1' UMP sing 408 n n C2' C3' UMP sing 409 n n C2' H2' UMP sing 410 n n C2' "H2''" UMP sing 411 n n C3' C4' UMP sing 412 n n C3' O3' UMP sing 413 n n C3' H3' UMP sing 414 n n C4' O4' UMP sing 415 n n C4' C5' UMP sing 416 n n C4' H4' UMP sing 417 n n O3' HO3' UMP sing 418 n n C5' O5' UMP sing 419 n n C5' H5' UMP sing 420 n n C5' "H5''" UMP sing 421 n n O5' P UMP sing 422 n n P OP1 UMP doub 423 n n P OP2 UMP sing 424 n n P OP3 UMP sing 425 n n OP2 HOP2 UMP sing 426 n n OP3 HOP3 UMP sing 427 n n # _atom_sites.entry_id 3IJZ _atom_sites.fract_transf_matrix[1][1] 0.012877 _atom_sites.fract_transf_matrix[1][2] 0.007435 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014869 _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] 0.004445 _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 15C A 1 468 468 15C 15C . C 3 UMP A 1 469 469 UMP UMP . D 4 HOH A 1 321 321 HOH HOH . D 4 HOH A 2 322 322 HOH HOH . D 4 HOH A 3 323 323 HOH HOH . D 4 HOH A 4 324 324 HOH HOH . D 4 HOH A 5 325 325 HOH HOH . D 4 HOH A 6 326 326 HOH HOH . D 4 HOH A 7 327 327 HOH HOH . D 4 HOH A 8 328 328 HOH HOH . D 4 HOH A 9 329 329 HOH HOH . D 4 HOH A 10 330 330 HOH HOH . D 4 HOH A 11 331 331 HOH HOH . D 4 HOH A 12 332 332 HOH HOH . D 4 HOH A 13 333 333 HOH HOH . D 4 HOH A 14 334 334 HOH HOH . D 4 HOH A 15 335 335 HOH HOH . D 4 HOH A 16 336 336 HOH HOH . D 4 HOH A 17 337 337 HOH HOH . D 4 HOH A 18 338 338 HOH HOH . D 4 HOH A 19 339 339 HOH HOH . D 4 HOH A 20 340 340 HOH HOH . D 4 HOH A 21 341 341 HOH HOH . D 4 HOH A 22 342 342 HOH HOH . D 4 HOH A 23 343 343 HOH HOH . D 4 HOH A 24 344 344 HOH HOH . D 4 HOH A 25 345 345 HOH HOH . D 4 HOH A 26 346 346 HOH HOH . D 4 HOH A 27 347 347 HOH HOH . D 4 HOH A 28 348 348 HOH HOH . D 4 HOH A 29 349 349 HOH HOH . D 4 HOH A 30 350 350 HOH HOH . D 4 HOH A 31 351 351 HOH HOH . D 4 HOH A 32 352 352 HOH HOH . D 4 HOH A 33 353 353 HOH HOH . D 4 HOH A 34 354 354 HOH HOH . D 4 HOH A 35 355 355 HOH HOH . D 4 HOH A 36 356 356 HOH HOH . D 4 HOH A 37 357 357 HOH HOH . D 4 HOH A 38 358 358 HOH HOH . D 4 HOH A 39 359 359 HOH HOH . D 4 HOH A 40 360 360 HOH HOH . D 4 HOH A 41 361 361 HOH HOH . D 4 HOH A 42 362 362 HOH HOH . D 4 HOH A 43 363 363 HOH HOH . D 4 HOH A 44 364 364 HOH HOH . D 4 HOH A 45 365 365 HOH HOH . D 4 HOH A 46 366 366 HOH HOH . D 4 HOH A 47 367 367 HOH HOH . D 4 HOH A 48 368 368 HOH HOH . D 4 HOH A 49 369 369 HOH HOH . D 4 HOH A 50 370 370 HOH HOH . D 4 HOH A 51 371 371 HOH HOH . D 4 HOH A 52 372 372 HOH HOH . D 4 HOH A 53 373 373 HOH HOH . D 4 HOH A 54 374 374 HOH HOH . D 4 HOH A 55 375 375 HOH HOH . D 4 HOH A 56 376 376 HOH HOH . D 4 HOH A 57 377 377 HOH HOH . D 4 HOH A 58 378 378 HOH HOH . D 4 HOH A 59 379 379 HOH HOH . D 4 HOH A 60 380 380 HOH HOH . D 4 HOH A 61 381 381 HOH HOH . D 4 HOH A 62 382 382 HOH HOH . D 4 HOH A 63 383 383 HOH HOH . D 4 HOH A 64 384 384 HOH HOH . D 4 HOH A 65 385 385 HOH HOH . D 4 HOH A 66 386 386 HOH HOH . D 4 HOH A 67 387 387 HOH HOH . D 4 HOH A 68 388 388 HOH HOH . D 4 HOH A 69 389 389 HOH HOH . D 4 HOH A 70 390 390 HOH HOH . D 4 HOH A 71 391 391 HOH HOH . D 4 HOH A 72 392 392 HOH HOH . D 4 HOH A 73 393 393 HOH HOH . D 4 HOH A 74 394 394 HOH HOH . D 4 HOH A 75 395 395 HOH HOH . D 4 HOH A 76 396 396 HOH HOH . D 4 HOH A 77 397 397 HOH HOH . D 4 HOH A 78 398 398 HOH HOH . D 4 HOH A 79 399 399 HOH HOH . D 4 HOH A 80 400 400 HOH HOH . D 4 HOH A 81 401 401 HOH HOH . D 4 HOH A 82 402 402 HOH HOH . D 4 HOH A 83 403 403 HOH HOH . D 4 HOH A 84 404 404 HOH HOH . D 4 HOH A 85 405 405 HOH HOH . D 4 HOH A 86 406 406 HOH HOH . D 4 HOH A 87 407 407 HOH HOH . D 4 HOH A 88 408 408 HOH HOH . D 4 HOH A 89 409 409 HOH HOH . D 4 HOH A 90 410 410 HOH HOH . D 4 HOH A 91 411 411 HOH HOH . D 4 HOH A 92 412 412 HOH HOH . D 4 HOH A 93 413 413 HOH HOH . D 4 HOH A 94 414 414 HOH HOH . D 4 HOH A 95 415 415 HOH HOH . D 4 HOH A 96 416 416 HOH HOH . D 4 HOH A 97 417 417 HOH HOH . D 4 HOH A 98 418 418 HOH HOH . D 4 HOH A 99 419 419 HOH HOH . D 4 HOH A 100 420 420 HOH HOH . D 4 HOH A 101 421 421 HOH HOH . D 4 HOH A 102 422 422 HOH HOH . D 4 HOH A 103 423 423 HOH HOH . D 4 HOH A 104 424 424 HOH HOH . D 4 HOH A 105 425 425 HOH HOH . D 4 HOH A 106 426 426 HOH HOH . D 4 HOH A 107 427 427 HOH HOH . D 4 HOH A 108 428 428 HOH HOH . D 4 HOH A 109 429 429 HOH HOH . D 4 HOH A 110 430 430 HOH HOH . D 4 HOH A 111 431 431 HOH HOH . D 4 HOH A 112 432 432 HOH HOH . D 4 HOH A 113 433 433 HOH HOH . D 4 HOH A 114 434 434 HOH HOH . D 4 HOH A 115 435 435 HOH HOH . D 4 HOH A 116 436 436 HOH HOH . D 4 HOH A 117 437 437 HOH HOH . D 4 HOH A 118 438 438 HOH HOH . D 4 HOH A 119 439 439 HOH HOH . D 4 HOH A 120 440 440 HOH HOH . D 4 HOH A 121 441 441 HOH HOH . D 4 HOH A 122 442 442 HOH HOH . D 4 HOH A 123 443 443 HOH HOH . D 4 HOH A 124 444 444 HOH HOH . D 4 HOH A 125 445 445 HOH HOH . D 4 HOH A 126 446 446 HOH HOH . D 4 HOH A 127 447 447 HOH HOH . D 4 HOH A 128 448 448 HOH HOH . D 4 HOH A 129 449 449 HOH HOH . D 4 HOH A 130 450 450 HOH HOH . D 4 HOH A 131 451 451 HOH HOH . D 4 HOH A 132 452 452 HOH HOH . D 4 HOH A 133 453 453 HOH HOH . D 4 HOH A 134 454 454 HOH HOH . D 4 HOH A 135 455 455 HOH HOH . D 4 HOH A 136 456 456 HOH HOH . D 4 HOH A 137 457 457 HOH HOH . D 4 HOH A 138 458 458 HOH HOH . D 4 HOH A 139 459 459 HOH HOH . D 4 HOH A 140 460 460 HOH HOH . D 4 HOH A 141 461 461 HOH HOH . D 4 HOH A 142 462 462 HOH HOH . D 4 HOH A 143 463 463 HOH HOH . D 4 HOH A 144 464 464 HOH HOH . D 4 HOH A 145 465 465 HOH HOH . D 4 HOH A 146 466 466 HOH HOH . D 4 HOH A 147 467 467 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 UMP . . . C 3 31.401 -9.614 24.092 1 63.44 ? N1 UMP 469 A 1 HETATM 2 C C2 UMP . . . C 3 32.53 -9.858 24.917 1 60.82 ? C2 UMP 469 A 1 HETATM 3 N N3 UMP . . . C 3 32.435 -10.829 25.883 1 62.19 ? N3 UMP 469 A 1 HETATM 4 C C4 UMP . . . C 3 31.264 -11.542 26.076 1 64.98 ? C4 UMP 469 A 1 HETATM 5 C C5 UMP . . . C 3 30.157 -11.305 25.288 1 64.75 ? C5 UMP 469 A 1 HETATM 6 C C6 UMP . . . C 3 30.25 -10.327 24.316 1 64.61 ? C6 UMP 469 A 1 HETATM 7 O O2 UMP . . . C 3 33.622 -9.291 24.873 1 55.58 ? O2 UMP 469 A 1 HETATM 8 O O4 UMP . . . C 3 31.173 -12.409 26.946 1 68.91 ? O4 UMP 469 A 1 HETATM 9 C C1' UMP . . . C 3 31.214 -8.613 22.993 1 63.84 ? C1' UMP 469 A 1 HETATM 10 C C2' UMP . . . C 3 32.039 -8.754 21.723 1 63.92 ? C2' UMP 469 A 1 HETATM 11 C C3' UMP . . . C 3 31.123 -8.184 20.643 1 62.97 ? C3' UMP 469 A 1 HETATM 12 C C4' UMP . . . C 3 29.738 -8.551 21.103 1 61.62 ? C4' UMP 469 A 1 HETATM 13 O O3' UMP . . . C 3 31.17 -6.766 20.602 1 63.08 ? O3' UMP 469 A 1 HETATM 14 O O4' UMP . . . C 3 29.868 -8.719 22.515 1 64.61 ? O4' UMP 469 A 1 HETATM 15 C C5' UMP . . . C 3 29.214 -9.799 20.379 1 56.55 ? C5' UMP 469 A 1 HETATM 16 O O5' UMP . . . C 3 28.364 -9.445 19.284 1 50.92 ? O5' UMP 469 A 1 HETATM 17 P P UMP . . . C 3 28.373 -10.328 17.946 1 37.65 ? P UMP 469 A 1 HETATM 18 O OP1 UMP . . . C 3 27.627 -9.751 16.823 1 39.9 ? OP1 UMP 469 A 1 HETATM 19 O OP2 UMP . . . C 3 27.758 -11.619 18.331 1 42.51 ? OP2 UMP 469 A 1 HETATM 20 O OP3 UMP . . . C 3 29.817 -10.371 17.647 1 42.61 ? OP3 UMP 469 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #