data_5CG8 # _model_server_result.job_id HkHg8Moa6mRm0wJvrfj0_A _model_server_result.datetime_utc '2025-03-09 02:32:07' _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 5cg8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5CG8 # _exptl.entry_id 5CG8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-OXOGLUTARIC ACID' _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 90 _cell.entry_id 5CG8 _cell.length_a 83.802 _cell.length_b 107.36 _cell.length_c 167.671 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CG8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 C O3' DA 5 C DA 19 1_555 C P 5HC 6 C 5HC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale2 C O3' 5HC 6 C 5HC 20 1_555 C P DG 7 C DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? metalc ? metalc1 A NE2 HIS 175 A HIS 229 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc2 A OD2 ASP 177 A ASP 231 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc3 A NE2 HIS 225 A HIS 279 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc4 D O2 AKG . A AKG 401 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc5 D O5 AKG . A AKG 401 1_555 E MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc6 E MN MN . A MN 402 1_555 F O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? hydrog WATSON-CRICK hydrog1 B N1 DA 1 B DA 1 1_555 C N3 DT 14 C DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 1 B DA 1 1_555 C O4 DT 14 C DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog3 B N1 DG 2 B DG 2 1_555 C N3 DC 13 C DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog4 B N1 DA 3 B DA 3 1_555 C N3 DT 12 C DT 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N1 DA 4 B DA 4 1_555 C N3 DT 11 C DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N6 DA 4 B DA 4 1_555 C O4 DT 11 C DT 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog7 B O4 DT 5 B DT 5 1_555 C N6 DA 9 C DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DT 5 B DT 5 1_555 C N1 DA 10 C DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O4 DT 5 B DT 5 1_555 C N6 DA 10 C DA 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DT 6 B DT 6 1_555 C N1 DA 9 C DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O4 DT 6 B DT 6 1_555 C N6 DA 9 C DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog12 B O2 DC 7 B DC 7 1_555 C N2 DG 8 C DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DC 8 B DC 8 1_555 C N1 DG 7 C DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N4 DC 8 B DC 8 1_555 C O6 DG 7 C DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O2 DC 8 B DC 8 1_555 C N2 DG 7 C DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog16 B N3 DT 10 B DT 10 1_555 C N1 DA 5 C DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 11 B DT 11 1_555 C N1 DA 4 C DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 11 B DT 11 1_555 C N6 DA 4 C DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog19 B O2 DC 12 B DC 12 1_555 C N2 DG 3 C DG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N3 DC 13 B DC 13 1_555 C N1 DG 2 C DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N4 DC 13 B DC 13 1_555 C O6 DG 2 C DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O2 DC 13 B DC 13 1_555 C N2 DG 2 C DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N1 DA 14 B DA 14 1_555 C N3 DT 1 C DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N6 DA 14 B DA 14 1_555 C O4 DT 1 C DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C5 H6 O5' _chem_comp.formula_weight 146.098 _chem_comp.id AKG _chem_comp.mon_nstd_flag . _chem_comp.name '2-OXOGLUTARIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 O1 AKG doub 40 n n C1 O2 AKG sing 41 n n C1 C2 AKG sing 42 n n O2 HO2 AKG sing 43 n n C2 O5 AKG doub 44 n n C2 C3 AKG sing 45 n n C3 C4 AKG sing 46 n n C3 H31 AKG sing 47 n n C3 H32 AKG sing 48 n n C4 C5 AKG sing 49 n n C4 H41 AKG sing 50 n n C4 H42 AKG sing 51 n n C5 O3 AKG doub 52 n n C5 O4 AKG sing 53 n n O4 HO4 AKG sing 54 n n # _atom_sites.entry_id 5CG8 _atom_sites.fract_transf_matrix[1][1] 0.011933 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009314 _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] 0.005964 _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 D 4 AKG A 1 401 1 AKG AKG . E 5 MN A 1 402 1 MN MN . F 6 HOH A 1 501 4 HOH HOH . F 6 HOH A 2 502 1 HOH HOH . F 6 HOH A 3 503 3 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 C C1 AKG . . . D 4 10.832 9.757 -20.709 1 81.74 ? C1 AKG 401 A 1 HETATM 2 O O1 AKG . . . D 4 9.859 9.365 -21.323 1 82.13 ? O1 AKG 401 A 1 HETATM 3 O O2 AKG . . . D 4 11.297 9.103 -19.627 1 78.29 ? O2 AKG 401 A 1 HETATM 4 C C2 AKG . . . D 4 11.571 10.987 -21.112 1 83.03 ? C2 AKG 401 A 1 HETATM 5 O O5 AKG . . . D 4 12.62 11.267 -20.582 1 84.97 ? O5 AKG 401 A 1 HETATM 6 C C3 AKG . . . D 4 10.992 11.871 -22.185 1 73.45 ? C3 AKG 401 A 1 HETATM 7 C C4 AKG . . . D 4 11.883 13.094 -22.433 1 71.94 ? C4 AKG 401 A 1 HETATM 8 C C5 AKG . . . D 4 11.21 14.134 -23.293 1 87.4 ? C5 AKG 401 A 1 HETATM 9 O O3 AKG . . . D 4 10.031 14.034 -23.551 1 90.55 ? O3 AKG 401 A 1 HETATM 10 O O4 AKG . . . D 4 11.913 15.17 -23.773 1 73.67 ? O4 AKG 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #