data_3BZ0 # _model_server_result.job_id xLumzNybOdEiMFibgisQSQ _model_server_result.datetime_utc '2024-10-10 21:28:59' _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 3bz0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 3BZ0 # _exptl.entry_id 3BZ0 _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 3BZ0 _cell.length_a 77.916 _cell.length_b 77.916 _cell.length_c 224.183 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BZ0 _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_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -38.958 67.477235 37.363833 # _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 3BZ0 _atom_sites.fract_transf_matrix[1][1] 0.012834 _atom_sites.fract_transf_matrix[1][2] 0.00741 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01482 _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] 0.004461 _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 6 HOH HOH . D 4 HOH A 6 324 7 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 12 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 17 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 23 HOH HOH . D 4 HOH A 21 339 24 HOH HOH . D 4 HOH A 22 340 25 HOH HOH . D 4 HOH A 23 341 26 HOH HOH . D 4 HOH A 24 342 27 HOH HOH . D 4 HOH A 25 343 28 HOH HOH . D 4 HOH A 26 344 29 HOH HOH . D 4 HOH A 27 345 30 HOH HOH . D 4 HOH A 28 346 31 HOH HOH . D 4 HOH A 29 347 32 HOH HOH . D 4 HOH A 30 348 33 HOH HOH . D 4 HOH A 31 349 34 HOH HOH . D 4 HOH A 32 350 36 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 . # 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 -31.226 9.5 23.904 1 78.76 ? N1 UMP 317 A 1 HETATM 2 C C2 UMP . . . B 2 -32.557 9.455 24.407 1 79.35 ? C2 UMP 317 A 1 HETATM 3 N N3 UMP . . . B 2 -32.909 10.179 25.534 1 79.21 ? N3 UMP 317 A 1 HETATM 4 C C4 UMP . . . B 2 -31.938 10.935 26.174 1 79.66 ? C4 UMP 317 A 1 HETATM 5 C C5 UMP . . . B 2 -30.627 10.982 25.709 1 79.76 ? C5 UMP 317 A 1 HETATM 6 C C6 UMP . . . B 2 -30.296 10.257 24.578 1 78.84 ? C6 UMP 317 A 1 HETATM 7 O O2 UMP . . . B 2 -33.473 8.807 23.903 1 79.51 ? O2 UMP 317 A 1 HETATM 8 O O4 UMP . . . B 2 -32.22 11.575 27.176 1 79.83 ? O4 UMP 317 A 1 HETATM 9 C C1' UMP . . . B 2 -30.652 8.766 22.707 1 77.02 ? C1' UMP 317 A 1 HETATM 10 C C2' UMP . . . B 2 -31.575 8.197 21.618 1 73.41 ? C2' UMP 317 A 1 HETATM 11 C C3' UMP . . . B 2 -30.716 8.232 20.354 1 70.68 ? C3' UMP 317 A 1 HETATM 12 C C4' UMP . . . B 2 -29.568 9.201 20.64 1 69.49 ? C4' UMP 317 A 1 HETATM 13 O O3' UMP . . . B 2 -30.232 6.945 20.032 1 67.79 ? O3' UMP 317 A 1 HETATM 14 O O4' UMP . . . B 2 -29.653 9.536 22.021 1 73.4 ? O4' UMP 317 A 1 HETATM 15 C C5' UMP . . . B 2 -29.684 10.485 19.801 1 63.94 ? C5' UMP 317 A 1 HETATM 16 O O5' UMP . . . B 2 -28.512 10.855 19.1 1 54.62 ? O5' UMP 317 A 1 HETATM 17 P P UMP . . . B 2 -28.403 10.33 17.6 1 48.87 ? P UMP 317 A 1 HETATM 18 O OP1 UMP . . . B 2 -27.054 10.64 17.028 1 49.54 ? OP1 UMP 317 A 1 HETATM 19 O OP2 UMP . . . B 2 -28.513 8.854 17.478 1 51.26 ? OP2 UMP 317 A 1 HETATM 20 O OP3 UMP . . . B 2 -29.547 10.863 16.841 1 51.63 ? OP3 UMP 317 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #