data_3BYX # _model_server_result.job_id h-szrQuh6YUtXNYyyD-ICQ _model_server_result.datetime_utc '2024-10-10 19:24:27' _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 3byx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 3BYX # _exptl.entry_id 3BYX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _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 3BYX _cell.length_a 77.012 _cell.length_b 77.012 _cell.length_c 213.97 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BYX _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' 10_554 -y,-x,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -35.661667 # _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 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 401 n n N1 C6 UMP sing 402 n n N1 C1' UMP sing 403 n n C2 N3 UMP sing 404 n n C2 O2 UMP doub 405 n n N3 C4 UMP sing 406 n n N3 HN3 UMP sing 407 n n C4 C5 UMP sing 408 n n C4 O4 UMP doub 409 n n C5 C6 UMP doub 410 n n C5 H5 UMP sing 411 n n C6 H6 UMP sing 412 n n C1' C2' UMP sing 413 n n C1' O4' UMP sing 414 n n C1' H1' UMP sing 415 n n C2' C3' UMP sing 416 n n C2' H2' UMP sing 417 n n C2' "H2''" UMP sing 418 n n C3' C4' UMP sing 419 n n C3' O3' UMP sing 420 n n C3' H3' UMP sing 421 n n C4' O4' UMP sing 422 n n C4' C5' UMP sing 423 n n C4' H4' UMP sing 424 n n O3' HO3' UMP sing 425 n n C5' O5' UMP sing 426 n n C5' H5' UMP sing 427 n n C5' "H5''" UMP sing 428 n n O5' P UMP sing 429 n n P OP1 UMP doub 430 n n P OP2 UMP sing 431 n n P OP3 UMP sing 432 n n OP2 HOP2 UMP sing 433 n n OP3 HOP3 UMP sing 434 n n # _atom_sites.entry_id 3BYX _atom_sites.fract_transf_matrix[1][1] 0.012985 _atom_sites.fract_transf_matrix[1][2] 0.007497 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014994 _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] 0.004674 _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 UMP A 1 317 317 UMP UMP . C 3 C00 A 1 318 1 C00 C20 . D 4 HOH A 1 319 1 HOH HOH . D 4 HOH A 2 320 2 HOH HOH . D 4 HOH A 3 321 3 HOH HOH . D 4 HOH A 4 322 4 HOH HOH . D 4 HOH A 5 323 5 HOH HOH . D 4 HOH A 6 324 6 HOH HOH . D 4 HOH A 7 325 8 HOH HOH . D 4 HOH A 8 326 9 HOH HOH . D 4 HOH A 9 327 10 HOH HOH . D 4 HOH A 10 328 11 HOH HOH . D 4 HOH A 11 329 13 HOH HOH . D 4 HOH A 12 330 14 HOH HOH . D 4 HOH A 13 331 15 HOH HOH . D 4 HOH A 14 332 16 HOH HOH . D 4 HOH A 15 333 18 HOH HOH . D 4 HOH A 16 334 19 HOH HOH . D 4 HOH A 17 335 20 HOH HOH . D 4 HOH A 18 336 21 HOH HOH . D 4 HOH A 19 337 22 HOH HOH . D 4 HOH A 20 338 24 HOH HOH . D 4 HOH A 21 339 25 HOH HOH . D 4 HOH A 22 340 26 HOH HOH . D 4 HOH A 23 341 27 HOH HOH . D 4 HOH A 24 342 28 HOH HOH . D 4 HOH A 25 343 29 HOH HOH . D 4 HOH A 26 344 30 HOH HOH . D 4 HOH A 27 345 32 HOH HOH . D 4 HOH A 28 346 33 HOH HOH . D 4 HOH A 29 347 34 HOH HOH . D 4 HOH A 30 348 36 HOH HOH . D 4 HOH A 31 349 37 HOH HOH . D 4 HOH A 32 350 39 HOH HOH . D 4 HOH A 33 351 40 HOH HOH . D 4 HOH A 34 352 41 HOH HOH . D 4 HOH A 35 353 42 HOH HOH . D 4 HOH A 36 354 43 HOH HOH . D 4 HOH A 37 355 44 HOH HOH . D 4 HOH A 38 356 45 HOH HOH . D 4 HOH A 39 357 46 HOH HOH . D 4 HOH A 40 358 47 HOH HOH . D 4 HOH A 41 359 48 HOH HOH . D 4 HOH A 42 360 49 HOH HOH . D 4 HOH A 43 361 50 HOH HOH . D 4 HOH A 44 362 51 HOH HOH . D 4 HOH A 45 363 52 HOH HOH . D 4 HOH A 46 364 54 HOH HOH . D 4 HOH A 47 365 55 HOH HOH . D 4 HOH A 48 366 56 HOH HOH . D 4 HOH A 49 367 57 HOH HOH . D 4 HOH A 50 368 58 HOH HOH . D 4 HOH A 51 369 59 HOH HOH . D 4 HOH A 52 370 60 HOH HOH . D 4 HOH A 53 371 61 HOH HOH . D 4 HOH A 54 372 62 HOH HOH . D 4 HOH A 55 373 63 HOH HOH . D 4 HOH A 56 374 64 HOH HOH . D 4 HOH A 57 375 65 HOH HOH . D 4 HOH A 58 376 66 HOH HOH . D 4 HOH A 59 377 67 HOH HOH . D 4 HOH A 60 378 68 HOH HOH . D 4 HOH A 61 379 69 HOH HOH . D 4 HOH A 62 380 70 HOH HOH . D 4 HOH A 63 381 71 HOH HOH . D 4 HOH A 64 382 75 HOH HOH . D 4 HOH A 65 383 76 HOH HOH . D 4 HOH A 66 384 77 HOH HOH . D 4 HOH A 67 385 78 HOH HOH . D 4 HOH A 68 386 80 HOH HOH . D 4 HOH A 69 387 83 HOH HOH . D 4 HOH A 70 388 84 HOH HOH . D 4 HOH A 71 389 87 HOH HOH . D 4 HOH A 72 390 88 HOH HOH . D 4 HOH A 73 391 90 HOH HOH . D 4 HOH A 74 392 91 HOH HOH . D 4 HOH A 75 393 93 HOH HOH . D 4 HOH A 76 394 94 HOH HOH . D 4 HOH A 77 395 96 HOH HOH . D 4 HOH A 78 396 97 HOH HOH . D 4 HOH A 79 397 98 HOH HOH . D 4 HOH A 80 398 99 HOH HOH . D 4 HOH A 81 399 100 HOH HOH . D 4 HOH A 82 400 101 HOH HOH . D 4 HOH A 83 401 102 HOH HOH . D 4 HOH A 84 402 103 HOH HOH . D 4 HOH A 85 403 104 HOH HOH . D 4 HOH A 86 404 105 HOH HOH . D 4 HOH A 87 405 106 HOH HOH . D 4 HOH A 88 406 107 HOH HOH . D 4 HOH A 89 407 108 HOH HOH . D 4 HOH A 90 408 109 HOH HOH . D 4 HOH A 91 409 110 HOH HOH . D 4 HOH A 92 410 111 HOH HOH . D 4 HOH A 93 411 112 HOH HOH . D 4 HOH A 94 412 113 HOH HOH . D 4 HOH A 95 413 114 HOH HOH . D 4 HOH A 96 414 115 HOH HOH . D 4 HOH A 97 415 116 HOH HOH . D 4 HOH A 98 416 117 HOH HOH . D 4 HOH A 99 417 119 HOH HOH . D 4 HOH A 100 418 121 HOH HOH . D 4 HOH A 101 419 122 HOH HOH . D 4 HOH A 102 420 125 HOH HOH . D 4 HOH A 103 421 126 HOH HOH . D 4 HOH A 104 422 127 HOH HOH . D 4 HOH A 105 423 128 HOH HOH . D 4 HOH A 106 424 129 HOH HOH . D 4 HOH A 107 425 130 HOH HOH . D 4 HOH A 108 426 131 HOH HOH . D 4 HOH A 109 427 132 HOH HOH . D 4 HOH A 110 428 133 HOH HOH . D 4 HOH A 111 429 134 HOH HOH . D 4 HOH A 112 430 135 HOH HOH . D 4 HOH A 113 431 137 HOH HOH . D 4 HOH A 114 432 138 HOH HOH . D 4 HOH A 115 433 139 HOH HOH . D 4 HOH A 116 434 140 HOH HOH . D 4 HOH A 117 435 141 HOH HOH . D 4 HOH A 118 436 142 HOH HOH . D 4 HOH A 119 437 143 HOH HOH . D 4 HOH A 120 438 144 HOH HOH . D 4 HOH A 121 439 146 HOH HOH . D 4 HOH A 122 440 147 HOH HOH . D 4 HOH A 123 441 148 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 . . . B 2 -27.964 33.902 -14.027 1 28.04 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 -27.513 32.827 -13.263 1 28.07 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 -28.229 32.399 -12.156 1 28.45 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 -29.394 33.078 -11.788 1 28.73 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 -29.837 34.165 -12.549 1 27.99 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 -29.101 34.583 -13.665 1 27.5 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 -26.485 32.234 -13.578 1 28.42 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 -30.035 32.729 -10.789 1 27.63 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 -27.182 34.391 -15.174 1 26.2 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 -27.142 33.526 -16.42 1 24.97 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 -26.941 34.587 -17.484 1 24.07 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 -27.69 35.793 -16.966 1 23.87 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 -25.57 34.928 -17.563 1 24.25 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 -27.67 35.666 -15.555 1 24.6 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 -29.135 35.749 -17.452 1 24.41 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 -29.215 36.232 -18.775 1 25.55 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 -30.131 35.486 -19.863 1 22.26 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 -31.592 35.692 -19.523 1 23.26 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 -29.813 35.954 -21.255 1 26.28 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 -29.814 34.044 -19.844 1 26.8 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #