data_3BUC # _model_server_result.job_id YDfsxD-PnJoLbDCiik6ftA _model_server_result.datetime_utc '2024-11-24 17:01:16' _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 3buc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":259}' # _entry.id 3BUC # _exptl.entry_id 3BUC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 6 _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 120 _cell.entry_id 3BUC _cell.length_a 77.91 _cell.length_b 77.91 _cell.length_c 226.558 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BUC _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H _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 6 _struct_asym.id F _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 A O3' DT 6 B DT 6 1_555 A P MA7 7 B MA7 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale2 A O3' MA7 7 B MA7 7 1_555 A P DA 8 B DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.591 ? covale ? covale3 A N4 DC 9 B DC 9 1_555 D CA XL3 . B XL3 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale4 D SG XL3 . B XL3 14 1_555 C SG CYS 114 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 E MN MN . A MN 1 1_555 C OD2 ASP 118 A ASP 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc2 E MN MN . A MN 1 1_555 F O5 AKG . A AKG 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc3 E MN MN . A MN 1 1_555 F O1 AKG . A AKG 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc4 E MN MN . A MN 1 1_555 H O HOH . A HOH 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? hydrog WATSON-CRICK hydrog1 A N1 DG 3 B DG 3 1_555 B N3 DC 12 C DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 3 B DG 3 1_555 B O2 DC 12 C DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 3 B DG 3 1_555 B N4 DC 12 C DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DT 4 B DT 4 1_555 B N1 DA 11 C DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O4 DT 4 B DT 4 1_555 B N6 DA 11 C DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog6 A N6 DA 5 B DA 5 1_555 B O4 DT 8 C DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DA 5 B DA 5 1_555 B N3 DT 10 C DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N6 DA 5 B DA 5 1_555 B O4 DT 10 C DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog9 A N3 DT 6 B DT 6 1_555 B O4 DT 8 C DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog10 A O2 DT 6 B DT 6 1_555 B N3 DT 8 C DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N1 DA 8 B DA 8 1_555 B N3 DT 7 C DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N6 DA 8 B DA 8 1_555 B O4 DT 7 C DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog13 A O2 DC 9 B DC 9 1_555 B N1 DG 6 C DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 DT 10 B DT 10 1_555 B N1 DA 5 C DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O4 DT 10 B DT 10 1_555 B N6 DA 5 C DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 11 B DG 11 1_555 B N3 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 11 B DG 11 1_555 B O2 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 11 B DG 11 1_555 B N4 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DC 12 B DC 12 1_555 B N1 DG 3 C DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N4 DC 12 B DC 12 1_555 B O6 DG 3 C DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O2 DC 12 B DC 12 1_555 B N2 DG 3 C DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 DG 13 B DG 13 1_555 B N3 DC 2 C DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N2 DG 13 B DG 13 1_555 B O2 DC 2 C DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O6 DG 13 B DG 13 1_555 B N4 DC 2 C DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog25 A N4 DC 1 B DC 1 1_555 A O6 DG 13 B DG 13 8_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog26 A O6 DG 13 B DG 13 1_555 A N4 DC 1 B DC 1 8_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 1 n n C1 O2 AKG sing 2 n n C1 C2 AKG sing 3 n n O2 HO2 AKG sing 4 n n C2 O5 AKG doub 5 n n C2 C3 AKG sing 6 n n C3 C4 AKG sing 7 n n C3 H31 AKG sing 8 n n C3 H32 AKG sing 9 n n C4 C5 AKG sing 10 n n C4 H41 AKG sing 11 n n C4 H42 AKG sing 12 n n C5 O3 AKG doub 13 n n C5 O4 AKG sing 14 n n O4 HO4 AKG sing 15 n n # _atom_sites.entry_id 3BUC _atom_sites.fract_transf_matrix[1][1] 0.012835 _atom_sites.fract_transf_matrix[1][2] 0.00741 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014821 _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] 0.004414 _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 XL3 B 1 14 1 XL3 XL3 . E 5 MN A 1 1 1 MN MN . F 6 AKG A 1 259 1 AKG AKG . G 7 HOH C 1 20 20 HOH HOH . G 7 HOH C 2 27 27 HOH HOH . G 7 HOH C 3 28 28 HOH HOH . G 7 HOH C 4 29 29 HOH HOH . G 7 HOH C 5 32 32 HOH HOH . H 7 HOH A 1 260 1 HOH HOH . H 7 HOH A 2 261 2 HOH HOH . H 7 HOH A 3 262 3 HOH HOH . H 7 HOH A 4 263 4 HOH HOH . H 7 HOH A 5 264 5 HOH HOH . H 7 HOH A 6 265 6 HOH HOH . H 7 HOH A 7 266 7 HOH HOH . H 7 HOH A 8 267 8 HOH HOH . H 7 HOH A 9 268 9 HOH HOH . H 7 HOH A 10 269 10 HOH HOH . H 7 HOH A 11 270 11 HOH HOH . H 7 HOH A 12 271 12 HOH HOH . H 7 HOH A 13 272 13 HOH HOH . H 7 HOH A 14 273 14 HOH HOH . H 7 HOH A 15 274 15 HOH HOH . H 7 HOH A 16 275 16 HOH HOH . H 7 HOH A 17 276 17 HOH HOH . H 7 HOH A 18 277 18 HOH HOH . H 7 HOH A 19 278 19 HOH HOH . H 7 HOH A 20 279 21 HOH HOH . H 7 HOH A 21 280 22 HOH HOH . H 7 HOH A 22 281 23 HOH HOH . H 7 HOH A 23 282 24 HOH HOH . H 7 HOH A 24 283 25 HOH HOH . H 7 HOH A 25 284 26 HOH HOH . H 7 HOH A 26 285 30 HOH HOH . H 7 HOH A 27 286 31 HOH HOH . H 7 HOH A 28 287 33 HOH HOH . H 7 HOH A 29 288 34 HOH HOH . H 7 HOH A 30 289 35 HOH HOH . H 7 HOH A 31 290 36 HOH HOH . H 7 HOH A 32 291 37 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 . . . F 6 -16.141 25.902 4.342 1 47.43 ? C1 AKG 259 A 1 HETATM 2 O O1 AKG . . . F 6 -15.704 25.325 5.365 1 48.11 ? O1 AKG 259 A 1 HETATM 3 O O2 AKG . . . F 6 -16.017 27.128 4.163 1 48.34 ? O2 AKG 259 A 1 HETATM 4 C C2 AKG . . . F 6 -16.822 25.11 3.329 1 46.67 ? C2 AKG 259 A 1 HETATM 5 O O5 AKG . . . F 6 -16.939 23.906 3.519 1 45.11 ? O5 AKG 259 A 1 HETATM 6 C C3 AKG . . . F 6 -17.351 25.81 2.089 1 45.72 ? C3 AKG 259 A 1 HETATM 7 C C4 AKG . . . F 6 -18.354 24.945 1.33 1 46.5 ? C4 AKG 259 A 1 HETATM 8 C C5 AKG . . . F 6 -18.853 25.599 0.056 1 46.47 ? C5 AKG 259 A 1 HETATM 9 O O3 AKG . . . F 6 -20.026 25.376 -0.297 1 46.63 ? O3 AKG 259 A 1 HETATM 10 O O4 AKG . . . F 6 -18.101 26.326 -0.624 1 46.19 ? O4 AKG 259 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 10 #