data_1VZD # _model_server_result.job_id qqxX8xKLvKv9oplq3mzFMw _model_server_result.datetime_utc '2024-12-12 07:43:50' _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 1vzd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1VZD # _exptl.entry_id 1VZD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 326.172 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-FLUORO-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 1VZD _cell.length_a 78.5 _cell.length_b 78.5 _cell.length_c 230.6 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VZD _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -115.3 # _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 H12 F N2 O8 P' _chem_comp.formula_weight 326.172 _chem_comp.id UFP _chem_comp.mon_nstd_flag . _chem_comp.name "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna 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 UFP sing 418 n n N1 C6 UFP sing 419 n n N1 C1' UFP sing 420 n n C2 N3 UFP sing 421 n n C2 O2 UFP doub 422 n n N3 C4 UFP sing 423 n n N3 HN3 UFP sing 424 n n C4 C5 UFP sing 425 n n C4 O4 UFP doub 426 n n C5 C6 UFP doub 427 n n C5 F5 UFP sing 428 n n C6 H6 UFP sing 429 n n C1' C2' UFP sing 430 n n C1' O4' UFP sing 431 n n C1' H1' UFP sing 432 n n C2' C3' UFP sing 433 n n C2' "H2'1" UFP sing 434 n n C2' "H2'2" UFP sing 435 n n C3' C4' UFP sing 436 n n C3' O3' UFP sing 437 n n C3' H3' UFP sing 438 n n C4' O4' UFP sing 439 n n C4' C5' UFP sing 440 n n C4' H4' UFP sing 441 n n O3' HO3' UFP sing 442 n n C5' O5' UFP sing 443 n n C5' "H5'1" UFP sing 444 n n C5' "H5'2" UFP sing 445 n n O5' P UFP sing 446 n n P O1P UFP doub 447 n n P O2P UFP sing 448 n n P O3P UFP sing 449 n n O2P HOP2 UFP sing 450 n n O3P HOP3 UFP sing 451 n n # _atom_sites.entry_id 1VZD _atom_sites.fract_transf_matrix[1][1] 0.012739 _atom_sites.fract_transf_matrix[1][2] 0.007355 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01471 _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] 0.004337 _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 UFP A 1 317 317 UFP UFP . C 3 CB3 A 1 318 318 CB3 CB3 . D 4 HOH A 1 319 319 HOH HOH . D 4 HOH A 2 320 320 HOH HOH . D 4 HOH A 3 321 321 HOH HOH . D 4 HOH A 4 322 322 HOH HOH . D 4 HOH A 5 323 323 HOH HOH . D 4 HOH A 6 324 324 HOH HOH . D 4 HOH A 7 325 325 HOH HOH . D 4 HOH A 8 326 326 HOH HOH . D 4 HOH A 9 327 327 HOH HOH . D 4 HOH A 10 328 328 HOH HOH . D 4 HOH A 11 330 330 HOH HOH . D 4 HOH A 12 331 331 HOH HOH . D 4 HOH A 13 332 332 HOH HOH . D 4 HOH A 14 333 333 HOH HOH . D 4 HOH A 15 334 334 HOH HOH . D 4 HOH A 16 335 335 HOH HOH . D 4 HOH A 17 336 336 HOH HOH . D 4 HOH A 18 337 337 HOH HOH . D 4 HOH A 19 338 338 HOH HOH . D 4 HOH A 20 339 339 HOH HOH . D 4 HOH A 21 340 340 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 25 346 346 HOH HOH . D 4 HOH A 26 347 347 HOH HOH . D 4 HOH A 27 348 348 HOH HOH . D 4 HOH A 28 349 349 HOH HOH . D 4 HOH A 29 351 351 HOH HOH . D 4 HOH A 30 353 353 HOH HOH . D 4 HOH A 31 354 354 HOH HOH . D 4 HOH A 32 355 355 HOH HOH . D 4 HOH A 33 356 356 HOH HOH . D 4 HOH A 34 357 357 HOH HOH . D 4 HOH A 35 358 358 HOH HOH . D 4 HOH A 36 359 359 HOH HOH . D 4 HOH A 37 360 360 HOH HOH . D 4 HOH A 38 361 361 HOH HOH . D 4 HOH A 39 362 362 HOH HOH . D 4 HOH A 40 363 363 HOH HOH . D 4 HOH A 41 364 364 HOH HOH . D 4 HOH A 42 365 365 HOH HOH . D 4 HOH A 43 366 366 HOH HOH . D 4 HOH A 44 367 367 HOH HOH . D 4 HOH A 45 368 368 HOH HOH . D 4 HOH A 46 369 369 HOH HOH . D 4 HOH A 47 370 370 HOH HOH . D 4 HOH A 48 371 371 HOH HOH . D 4 HOH A 49 372 372 HOH HOH . D 4 HOH A 50 373 373 HOH HOH . D 4 HOH A 51 374 374 HOH HOH . D 4 HOH A 52 375 375 HOH HOH . D 4 HOH A 53 376 376 HOH HOH . D 4 HOH A 54 377 377 HOH HOH . D 4 HOH A 55 378 378 HOH HOH . D 4 HOH A 56 379 379 HOH HOH . D 4 HOH A 57 380 380 HOH HOH . D 4 HOH A 58 381 381 HOH HOH . D 4 HOH A 59 382 382 HOH HOH . D 4 HOH A 60 383 383 HOH HOH . D 4 HOH A 61 384 384 HOH HOH . D 4 HOH A 62 385 385 HOH HOH . D 4 HOH A 63 386 386 HOH HOH . D 4 HOH A 64 387 387 HOH HOH . D 4 HOH A 65 388 388 HOH HOH . D 4 HOH A 66 389 389 HOH HOH . D 4 HOH A 67 390 390 HOH HOH . D 4 HOH A 68 391 391 HOH HOH . D 4 HOH A 69 392 392 HOH HOH . D 4 HOH A 70 393 393 HOH HOH . D 4 HOH A 71 394 394 HOH HOH . D 4 HOH A 72 395 395 HOH HOH . D 4 HOH A 73 396 396 HOH HOH . D 4 HOH A 74 397 397 HOH HOH . D 4 HOH A 75 398 398 HOH HOH . D 4 HOH A 76 399 399 HOH HOH . D 4 HOH A 77 400 400 HOH HOH . D 4 HOH A 78 401 401 HOH HOH . D 4 HOH A 79 402 402 HOH HOH . D 4 HOH A 80 403 403 HOH HOH . D 4 HOH A 81 404 404 HOH HOH . D 4 HOH A 82 405 405 HOH HOH . D 4 HOH A 83 406 406 HOH HOH . D 4 HOH A 84 407 407 HOH HOH . D 4 HOH A 85 408 408 HOH HOH . D 4 HOH A 86 409 409 HOH HOH . D 4 HOH A 87 410 410 HOH HOH . D 4 HOH A 88 411 411 HOH HOH . D 4 HOH A 89 412 412 HOH HOH . D 4 HOH A 90 413 413 HOH HOH . D 4 HOH A 91 414 414 HOH HOH . D 4 HOH A 92 415 415 HOH HOH . D 4 HOH A 93 416 416 HOH HOH . D 4 HOH A 94 417 417 HOH HOH . D 4 HOH A 95 418 418 HOH HOH . D 4 HOH A 96 419 419 HOH HOH . D 4 HOH A 97 420 420 HOH HOH . D 4 HOH A 98 421 421 HOH HOH . D 4 HOH A 99 422 422 HOH HOH . D 4 HOH A 100 423 423 HOH HOH . D 4 HOH A 101 424 424 HOH HOH . D 4 HOH A 102 425 425 HOH HOH . D 4 HOH A 103 426 426 HOH HOH . D 4 HOH A 104 427 427 HOH HOH . D 4 HOH A 105 428 428 HOH HOH . D 4 HOH A 106 429 429 HOH HOH . D 4 HOH A 107 430 430 HOH HOH . D 4 HOH A 108 431 431 HOH HOH . D 4 HOH A 109 432 432 HOH HOH . D 4 HOH A 110 433 433 HOH HOH . D 4 HOH A 111 434 434 HOH HOH . D 4 HOH A 112 435 435 HOH HOH . D 4 HOH A 113 436 436 HOH HOH . D 4 HOH A 114 437 437 HOH HOH . D 4 HOH A 115 438 438 HOH HOH . D 4 HOH A 116 439 439 HOH HOH . D 4 HOH A 117 440 440 HOH HOH . D 4 HOH A 118 441 441 HOH HOH . D 4 HOH A 119 442 442 HOH HOH . D 4 HOH A 120 443 443 HOH HOH . D 4 HOH A 121 444 444 HOH HOH . D 4 HOH A 122 445 445 HOH HOH . D 4 HOH A 123 446 446 HOH HOH . D 4 HOH A 124 447 447 HOH HOH . D 4 HOH A 125 448 448 HOH HOH . D 4 HOH A 126 449 449 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 UFP . . . B 2 16.023 48.688 -51.886 1 17.9 ? N1 UFP 317 A 1 HETATM 2 C C2 UFP . . . B 2 14.876 47.888 -51.602 1 17.11 ? C2 UFP 317 A 1 HETATM 3 N N3 UFP . . . B 2 13.921 48.438 -50.75 1 17.16 ? N3 UFP 317 A 1 HETATM 4 C C4 UFP . . . B 2 14.03 49.691 -50.142 1 19.49 ? C4 UFP 317 A 1 HETATM 5 C C5 UFP . . . B 2 15.266 50.457 -50.469 1 18.81 ? C5 UFP 317 A 1 HETATM 6 C C6 UFP . . . B 2 16.225 49.893 -51.339 1 17.67 ? C6 UFP 317 A 1 HETATM 7 O O2 UFP . . . B 2 14.808 46.684 -51.834 1 15.61 ? O2 UFP 317 A 1 HETATM 8 O O4 UFP . . . B 2 13.143 50.046 -49.346 1 22.92 ? O4 UFP 317 A 1 HETATM 9 F F5 UFP . . . B 2 15.443 51.684 -50.002 1 13.56 ? F5 UFP 317 A 1 HETATM 10 C C1' UFP . . . B 2 16.969 48.328 -53.006 1 18.14 ? C1' UFP 317 A 1 HETATM 11 C C2' UFP . . . B 2 17.377 46.911 -53.296 1 17.05 ? C2' UFP 317 A 1 HETATM 12 C C3' UFP . . . B 2 16.422 46.55 -54.355 1 15.06 ? C3' UFP 317 A 1 HETATM 13 C C4' UFP . . . B 2 16.603 47.806 -55.263 1 16.43 ? C4' UFP 317 A 1 HETATM 14 O O3' UFP . . . B 2 16.786 45.347 -55.013 1 12.93 ? O3' UFP 317 A 1 HETATM 15 O O4' UFP . . . B 2 16.756 48.935 -54.339 1 15.7 ? O4' UFP 317 A 1 HETATM 16 C C5' UFP . . . B 2 15.432 48.071 -56.103 1 15.29 ? C5' UFP 317 A 1 HETATM 17 O O5' UFP . . . B 2 15.857 48.129 -57.505 1 14.46 ? O5' UFP 317 A 1 HETATM 18 P P UFP . . . B 2 16.21 49.539 -58.253 1 15.66 ? P UFP 317 A 1 HETATM 19 O O1P UFP . . . B 2 15.811 50.644 -57.324 1 14.69 ? O1P UFP 317 A 1 HETATM 20 O O2P UFP . . . B 2 17.671 49.345 -58.466 1 17.08 ? O2P UFP 317 A 1 HETATM 21 O O3P UFP . . . B 2 15.405 49.502 -59.471 1 13.99 ? O3P UFP 317 A 1 HETATM 22 H HN3 UFP . . . B 2 13.128 47.902 -50.569 1 15 ? HN3 UFP 317 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 22 #