data_9DKO # _model_server_result.job_id v1vluAJPaFRg8ve54wowEA _model_server_result.datetime_utc '2025-02-01 16:59:33' _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 9dko # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1003}' # _entry.id 9DKO # _exptl.entry_id 9DKO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 158.112 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-[bis(oxidanyl)methyl]-5~{H}-pyrimidine-2,4-dione _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 9DKO _cell.length_a 85.203 _cell.length_b 85.203 _cell.length_c 140.127 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DKO _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall 'P 64' _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C5 H6 N2 O4' _chem_comp.formula_weight 158.112 _chem_comp.id OG6 _chem_comp.mon_nstd_flag . _chem_comp.name 6-[bis(oxidanyl)methyl]-5~{H}-pyrimidine-2,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '6-Formyl-uracil hydrate' # 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 O01 C08 OG6 doub 336 n n N05 C08 OG6 sing 337 n n N05 C09 OG6 sing 338 n n C08 N04 OG6 sing 339 n n O02 C09 OG6 doub 340 n n C09 C07 OG6 sing 341 n n N04 C06 OG6 sing 342 n n C07 C06 OG6 doub 343 n n C06 C10 OG6 sing 344 n n C10 O2 OG6 sing 345 n n C10 H1 OG6 sing 346 n n C07 H2 OG6 sing 347 n n N05 H4 OG6 sing 348 n n C10 O1 OG6 sing 349 n n O2 H5 OG6 sing 350 n n O1 H6 OG6 sing 351 n n N04 H3 OG6 sing 352 n n # _atom_sites.entry_id 9DKO _atom_sites.fract_transf_matrix[1][1] 0.011737 _atom_sites.fract_transf_matrix[1][2] 0.006776 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013552 _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] 0.007136 _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 A1A5P A 1 1001 1001 A1A5P 010 . C 3 FMN A 1 1002 1002 FMN FMN . D 4 OG6 A 1 1003 1003 OG6 ORO . # 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 O O2 OG6 . . . D 4 13.092 -10.692 8.503 1 44.69 ? O2 OG6 1003 A 1 HETATM 2 C C10 OG6 . . . D 4 12.64 -11.827 8.71 1 47.16 ? C10 OG6 1003 A 1 HETATM 3 C C06 OG6 . . . D 4 13.142 -12.945 7.787 1 34.96 ? C06 OG6 1003 A 1 HETATM 4 C C07 OG6 . . . D 4 13.077 -12.902 6.442 1 34.42 ? C07 OG6 1003 A 1 HETATM 5 C C09 OG6 . . . D 4 13.574 -14.012 5.666 1 33.69 ? C09 OG6 1003 A 1 HETATM 6 O O02 OG6 . . . D 4 13.567 -14.086 4.448 1 23.73 ? O02 OG6 1003 A 1 HETATM 7 N N05 OG6 . . . D 4 14.09 -15.055 6.426 1 28.34 ? N05 OG6 1003 A 1 HETATM 8 C C08 OG6 . . . D 4 14.166 -15.125 7.794 1 32.09 ? C08 OG6 1003 A 1 HETATM 9 O O01 OG6 . . . D 4 14.635 -16.08 8.381 1 28.02 ? O01 OG6 1003 A 1 HETATM 10 N N04 OG6 . . . D 4 13.666 -14.023 8.426 1 34.68 ? N04 OG6 1003 A 1 HETATM 11 O O1 OG6 . . . D 4 11.824 -12.208 9.567 1 47.76 ? O1 OG6 1003 A 1 HETATM 12 H H2 OG6 . . . D 4 12.715 -12.165 6.005 1 41.49 ? H2 OG6 1003 A 1 HETATM 13 H H4 OG6 . . . D 4 14.396 -15.734 5.997 1 34.19 ? H4 OG6 1003 A 1 HETATM 14 H H3 OG6 . . . D 4 13.678 -13.994 9.286 1 41.8 ? H3 OG6 1003 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #