data_9DKY # _model_server_result.job_id xvYSGCApgw4-9WujotjZBg _model_server_result.datetime_utc '2025-01-08 10:30:10' _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 9dky # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1003}' # _entry.id 9DKY # _exptl.entry_id 9DKY _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 9DKY _cell.length_a 85.303 _cell.length_b 85.303 _cell.length_c 140.703 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DKY _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 349 n n N05 C08 OG6 sing 350 n n N05 C09 OG6 sing 351 n n C08 N04 OG6 sing 352 n n O02 C09 OG6 doub 353 n n C09 C07 OG6 sing 354 n n N04 C06 OG6 sing 355 n n C07 C06 OG6 doub 356 n n C06 C10 OG6 sing 357 n n C10 O2 OG6 sing 358 n n C10 H1 OG6 sing 359 n n C07 H2 OG6 sing 360 n n N05 H4 OG6 sing 361 n n C10 O1 OG6 sing 362 n n O2 H5 OG6 sing 363 n n O1 H6 OG6 sing 364 n n N04 H3 OG6 sing 365 n n # _atom_sites.entry_id 9DKY _atom_sites.fract_transf_matrix[1][1] 0.011723 _atom_sites.fract_transf_matrix[1][2] 0.006768 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013536 _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] 0.007107 _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 A1A59 A 1 1001 1001 A1A59 174 . 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 13.371 -10.832 8.706 1 29.65 ? O2 OG6 1003 A 1 HETATM 2 C C10 OG6 . . . D 4 12.876 -11.938 8.935 1 28.36 ? C10 OG6 1003 A 1 HETATM 3 C C06 OG6 . . . D 4 13.285 -13.078 7.989 1 30.74 ? C06 OG6 1003 A 1 HETATM 4 C C07 OG6 . . . D 4 13.153 -13.027 6.653 1 34.92 ? C07 OG6 1003 A 1 HETATM 5 C C09 OG6 . . . D 4 13.565 -14.155 5.851 1 33.99 ? C09 OG6 1003 A 1 HETATM 6 O O02 OG6 . . . D 4 13.498 -14.225 4.642 1 34.47 ? O02 OG6 1003 A 1 HETATM 7 N N05 OG6 . . . D 4 14.075 -15.224 6.576 1 41.24 ? N05 OG6 1003 A 1 HETATM 8 C C08 OG6 . . . D 4 14.216 -15.3 7.935 1 51.63 ? C08 OG6 1003 A 1 HETATM 9 O O01 OG6 . . . D 4 14.67 -16.271 8.487 1 47.31 ? O01 OG6 1003 A 1 HETATM 10 N N04 OG6 . . . D 4 13.796 -14.182 8.596 1 46.34 ? N04 OG6 1003 A 1 HETATM 11 O O1 OG6 . . . D 4 12.081 -12.288 9.819 1 39.4 ? O1 OG6 1003 A 1 HETATM 12 H H2 OG6 . . . D 4 12.8 -12.274 6.237 1 41.9 ? H2 OG6 1003 A 1 HETATM 13 H H4 OG6 . . . D 4 14.33 -15.913 6.129 1 49.49 ? H4 OG6 1003 A 1 HETATM 14 H H3 OG6 . . . D 4 13.852 -14.159 9.454 1 55.6 ? H3 OG6 1003 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #