data_9DI6 # _model_server_result.job_id QiIFLApWWflj0uv5f-OgPA _model_server_result.datetime_utc '2025-01-08 10:20:53' _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 9di6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1003}' # _entry.id 9DI6 # _exptl.entry_id 9DI6 _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 9DI6 _cell.length_a 73.768 _cell.length_b 73.768 _cell.length_c 328.285 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DI6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _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,E,F,G _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 397 n n N05 C08 OG6 sing 398 n n N05 C09 OG6 sing 399 n n C08 N04 OG6 sing 400 n n O02 C09 OG6 doub 401 n n C09 C07 OG6 sing 402 n n N04 C06 OG6 sing 403 n n C07 C06 OG6 doub 404 n n C06 C10 OG6 sing 405 n n C10 O2 OG6 sing 406 n n C10 H1 OG6 sing 407 n n C07 H2 OG6 sing 408 n n N05 H4 OG6 sing 409 n n C10 O1 OG6 sing 410 n n O2 H5 OG6 sing 411 n n O1 H6 OG6 sing 412 n n N04 H3 OG6 sing 413 n n # _atom_sites.entry_id 9DI6 _atom_sites.fract_transf_matrix[1][1] 0.013556 _atom_sites.fract_transf_matrix[1][2] 0.007827 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015653 _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] 0.003046 _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 A1A51 A 1 1001 1001 A1A51 679 . C 3 FMN A 1 1002 1002 FMN FMN . D 4 OG6 A 1 1003 1003 OG6 ORO . E 5 CIT A 1 1004 1004 CIT CIT . F 6 LDA A 1 1005 2001 LDA LDA . G 7 HOH A 1 1101 16 HOH HOH . G 7 HOH A 2 1102 7 HOH HOH . G 7 HOH A 3 1103 32 HOH HOH . G 7 HOH A 4 1104 14 HOH HOH . G 7 HOH A 5 1105 27 HOH HOH . G 7 HOH A 6 1106 8 HOH HOH . G 7 HOH A 7 1107 23 HOH HOH . G 7 HOH A 8 1108 9 HOH HOH . G 7 HOH A 9 1109 5 HOH HOH . G 7 HOH A 10 1110 28 HOH HOH . G 7 HOH A 11 1111 11 HOH HOH . G 7 HOH A 12 1112 36 HOH HOH . G 7 HOH A 13 1113 3 HOH HOH . G 7 HOH A 14 1114 17 HOH HOH . G 7 HOH A 15 1115 13 HOH HOH . G 7 HOH A 16 1116 1 HOH HOH . G 7 HOH A 17 1117 15 HOH HOH . G 7 HOH A 18 1118 19 HOH HOH . G 7 HOH A 19 1119 10 HOH HOH . G 7 HOH A 20 1120 4 HOH HOH . G 7 HOH A 21 1121 25 HOH HOH . G 7 HOH A 22 1122 24 HOH HOH . G 7 HOH A 23 1123 6 HOH HOH . G 7 HOH A 24 1124 21 HOH HOH . G 7 HOH A 25 1125 2 HOH HOH . G 7 HOH A 26 1126 22 HOH HOH . G 7 HOH A 27 1127 12 HOH HOH . G 7 HOH A 28 1128 18 HOH HOH . G 7 HOH A 29 1129 35 HOH HOH . G 7 HOH A 30 1130 29 HOH HOH . G 7 HOH A 31 1131 20 HOH HOH . G 7 HOH A 32 1132 30 HOH HOH . G 7 HOH A 33 1133 33 HOH HOH . G 7 HOH A 34 1134 31 HOH HOH . G 7 HOH A 35 1135 34 HOH HOH . G 7 HOH A 36 1136 26 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 O O2 OG6 . . . D 4 3.384 20.549 -4.311 1 32.76 ? O2 OG6 1003 A 1 HETATM 2 C C10 OG6 . . . D 4 4.358 20.677 -5.06 1 31.51 ? C10 OG6 1003 A 1 HETATM 3 C C06 OG6 . . . D 4 4.071 20.594 -6.568 1 26.33 ? C06 OG6 1003 A 1 HETATM 4 C C07 OG6 . . . D 4 3.141 19.783 -7.114 1 23.05 ? C07 OG6 1003 A 1 HETATM 5 C C09 OG6 . . . D 4 2.953 19.766 -8.544 1 27.91 ? C09 OG6 1003 A 1 HETATM 6 O O02 OG6 . . . D 4 2.145 19.073 -9.146 1 31.24 ? O02 OG6 1003 A 1 HETATM 7 N N05 OG6 . . . D 4 3.794 20.632 -9.239 1 23.35 ? N05 OG6 1003 A 1 HETATM 8 C C08 OG6 . . . D 4 4.75 21.468 -8.712 1 41.46 ? C08 OG6 1003 A 1 HETATM 9 O O01 OG6 . . . D 4 5.442 22.195 -9.402 1 31.17 ? O01 OG6 1003 A 1 HETATM 10 N N04 OG6 . . . D 4 4.842 21.401 -7.348 1 31.44 ? N04 OG6 1003 A 1 HETATM 11 O O1 OG6 . . . D 4 5.555 20.846 -4.768 1 37.73 ? O1 OG6 1003 A 1 HETATM 12 H H2 OG6 . . . D 4 2.616 19.233 -6.579 1 27.72 ? H2 OG6 1003 A 1 HETATM 13 H H4 OG6 . . . D 4 3.71 20.649 -10.095 1 28.08 ? H4 OG6 1003 A 1 HETATM 14 H H3 OG6 . . . D 4 5.419 21.893 -6.943 1 37.8 ? H3 OG6 1003 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #