data_9DKQ # _model_server_result.job_id 0yeFAezGqqok8GoyZ_O6EQ _model_server_result.datetime_utc '2025-01-07 09:32:58' _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 9dkq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1003}' # _entry.id 9DKQ # _exptl.entry_id 9DKQ _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 9DKQ _cell.length_a 85.615 _cell.length_b 85.615 _cell.length_c 140.161 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DKQ _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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 37 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 175 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 46 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 184 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.046 _struct_conn.pdbx_value_order ? # _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 340 n n N05 C08 OG6 sing 341 n n N05 C09 OG6 sing 342 n n C08 N04 OG6 sing 343 n n O02 C09 OG6 doub 344 n n C09 C07 OG6 sing 345 n n N04 C06 OG6 sing 346 n n C07 C06 OG6 doub 347 n n C06 C10 OG6 sing 348 n n C10 O2 OG6 sing 349 n n C10 H1 OG6 sing 350 n n C07 H2 OG6 sing 351 n n N05 H4 OG6 sing 352 n n C10 O1 OG6 sing 353 n n O2 H5 OG6 sing 354 n n O1 H6 OG6 sing 355 n n N04 H3 OG6 sing 356 n n # _atom_sites.entry_id 9DKQ _atom_sites.fract_transf_matrix[1][1] 0.01168 _atom_sites.fract_transf_matrix[1][2] 0.006744 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013487 _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] 0.007135 _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 A1A5Q A 1 1001 1001 A1A5Q 153 . 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 -3.168 -16.766 19.356 1 43.29 ? O2 OG6 1003 A 1 HETATM 2 C C10 OG6 . . . D 4 -4.317 -17.126 19.637 1 38.48 ? C10 OG6 1003 A 1 HETATM 3 C C06 OG6 . . . D 4 -4.984 -18.091 18.648 1 13.33 ? C06 OG6 1003 A 1 HETATM 4 C C07 OG6 . . . D 4 -4.837 -18.017 17.311 1 17.93 ? C07 OG6 1003 A 1 HETATM 5 C C09 OG6 . . . D 4 -5.509 -18.97 16.464 1 25.34 ? C09 OG6 1003 A 1 HETATM 6 O O02 OG6 . . . D 4 -5.45 -19.002 15.248 1 21.44 ? O02 OG6 1003 A 1 HETATM 7 N N05 OG6 . . . D 4 -6.271 -19.905 17.149 1 28.44 ? N05 OG6 1003 A 1 HETATM 8 C C08 OG6 . . . D 4 -6.44 -20.004 18.506 1 22.48 ? C08 OG6 1003 A 1 HETATM 9 O O01 OG6 . . . D 4 -7.129 -20.859 19.026 1 21.47 ? O01 OG6 1003 A 1 HETATM 10 N N04 OG6 . . . D 4 -5.761 -19.053 19.21 1 15.82 ? N04 OG6 1003 A 1 HETATM 11 O O1 OG6 . . . D 4 -5.023 -16.814 20.611 1 24.85 ? O1 OG6 1003 A 1 HETATM 12 H H2 OG6 . . . D 4 -4.307 -17.357 16.925 1 21.52 ? H2 OG6 1003 A 1 HETATM 13 H H4 OG6 . . . D 4 -6.685 -20.491 16.674 1 34.13 ? H4 OG6 1003 A 1 HETATM 14 H H3 OG6 . . . D 4 -5.818 -19.05 20.068 1 18.98 ? H3 OG6 1003 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 183 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #