data_3RZJ # _model_server_result.job_id z7lMQbNqoztpN2q0py2Gvw _model_server_result.datetime_utc '2024-11-13 20:44:48' _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 3rzj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":262}' # _entry.id 3RZJ # _exptl.entry_id 3RZJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 5 _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 3RZJ _cell.length_a 77.779 _cell.length_b 77.779 _cell.length_c 229.016 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RZJ _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,I _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 5 _struct_asym.id E _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 B O3' DT 6 B DT 264 1_555 B P ME6 7 B ME6 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? covale ? covale2 B O3' ME6 7 B ME6 265 1_555 B P DA 8 B DA 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.593 ? metalc ? metalc1 D MN MN . A MN 1 1_555 A NE2 HIS 119 A HIS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc2 D MN MN . A MN 1 1_555 A OD2 ASP 121 A ASP 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc3 D MN MN . A MN 1 1_555 A NE2 HIS 184 A HIS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc4 D MN MN . A MN 1 1_555 E O2 AKG . A AKG 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc5 D MN MN . A MN 1 1_555 E O5 AKG . A AKG 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? hydrog WATSON-CRICK hydrog1 B N1 DG 3 B DG 261 1_555 C N3 DC 12 C DC 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 3 B DG 261 1_555 C O2 DC 12 C DC 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 3 B DG 261 1_555 C N4 DC 12 C DC 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 4 B DT 262 1_555 C N1 DA 11 C DA 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 4 B DT 262 1_555 C N6 DA 11 C DA 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 5 B DC 263 1_555 C N1 DG 10 C DG 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 5 B DC 263 1_555 C O6 DG 10 C DG 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 5 B DC 263 1_555 C N2 DG 10 C DG 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DT 6 B DT 264 1_555 C N1 DA 9 C DA 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O4 DT 6 B DT 264 1_555 C N6 DA 9 C DA 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DA 8 B DA 266 1_555 C N3 DT 7 C DT 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N6 DA 8 B DA 266 1_555 C O4 DT 7 C DT 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N3 DC 9 B DC 267 1_555 C N1 DG 6 C DG 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N4 DC 9 B DC 267 1_555 C O6 DG 6 C DG 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O2 DC 9 B DC 267 1_555 C N2 DG 6 C DG 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DT 10 B DT 268 1_555 C N1 DA 5 C DA 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 DT 10 B DT 268 1_555 C N6 DA 5 C DA 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N1 DG 11 B DG 269 1_555 C N3 DC 4 C DC 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N2 DG 11 B DG 269 1_555 C O2 DC 4 C DC 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O6 DG 11 B DG 269 1_555 C N4 DC 4 C DC 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 12 B DC 270 1_555 C N1 DG 3 C DG 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 12 B DC 270 1_555 C O6 DG 3 C DG 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 12 B DC 270 1_555 C N2 DG 3 C DG 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N1 DG 13 B DG 271 1_555 C N3 DC 2 C DC 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N2 DG 13 B DG 271 1_555 C O2 DC 2 C DC 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O6 DG 13 B DG 271 1_555 C N4 DC 2 C DC 273 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 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 3RZJ _atom_sites.fract_transf_matrix[1][1] 0.012857 _atom_sites.fract_transf_matrix[1][2] 0.007423 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014846 _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] 0.004367 _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 MN A 1 1 1 MN MN . E 5 AKG A 1 262 1 AKG AKG . F 6 XL3 A 1 263 1 XL3 XL3 . G 7 HOH A 1 2 2 HOH HOH . G 7 HOH A 2 3 3 HOH HOH . G 7 HOH A 3 4 4 HOH HOH . G 7 HOH A 4 5 5 HOH HOH . G 7 HOH A 5 6 6 HOH HOH . G 7 HOH A 6 7 7 HOH HOH . G 7 HOH A 7 8 8 HOH HOH . G 7 HOH A 8 9 9 HOH HOH . G 7 HOH A 9 10 10 HOH HOH . G 7 HOH A 10 11 11 HOH HOH . G 7 HOH A 11 12 12 HOH HOH . G 7 HOH A 12 13 13 HOH HOH . G 7 HOH A 13 14 14 HOH HOH . G 7 HOH A 14 15 15 HOH HOH . G 7 HOH A 15 16 16 HOH HOH . G 7 HOH A 16 18 18 HOH HOH . G 7 HOH A 17 19 19 HOH HOH . G 7 HOH A 18 20 20 HOH HOH . G 7 HOH A 19 21 21 HOH HOH . G 7 HOH A 20 22 22 HOH HOH . G 7 HOH A 21 24 24 HOH HOH . G 7 HOH A 22 25 25 HOH HOH . G 7 HOH A 23 26 26 HOH HOH . G 7 HOH A 24 27 27 HOH HOH . G 7 HOH A 25 28 28 HOH HOH . G 7 HOH A 26 29 29 HOH HOH . G 7 HOH A 27 30 30 HOH HOH . G 7 HOH A 28 31 31 HOH HOH . G 7 HOH A 29 32 32 HOH HOH . G 7 HOH A 30 33 33 HOH HOH . G 7 HOH A 31 34 34 HOH HOH . G 7 HOH A 32 35 35 HOH HOH . G 7 HOH A 33 38 38 HOH HOH . G 7 HOH A 34 39 39 HOH HOH . G 7 HOH A 35 40 40 HOH HOH . G 7 HOH A 36 43 43 HOH HOH . G 7 HOH A 37 44 44 HOH HOH . G 7 HOH A 38 264 1 HOH HOH . H 7 HOH B 1 17 17 HOH HOH . H 7 HOH B 2 41 41 HOH HOH . I 7 HOH C 1 23 23 HOH HOH . I 7 HOH C 2 36 36 HOH HOH . I 7 HOH C 3 37 37 HOH HOH . I 7 HOH C 4 42 42 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 . . . E 5 16.286 -26.193 4.329 1 51.11 ? C1 AKG 262 A 1 HETATM 2 O O1 AKG . . . E 5 16.523 -27.423 4.245 1 53.24 ? O1 AKG 262 A 1 HETATM 3 O O2 AKG . . . E 5 15.781 -25.69 5.353 1 51.97 ? O2 AKG 262 A 1 HETATM 4 C C2 AKG . . . E 5 16.597 -25.296 3.224 1 49.6 ? C2 AKG 262 A 1 HETATM 5 O O5 AKG . . . E 5 16.465 -24.092 3.394 1 49.36 ? O5 AKG 262 A 1 HETATM 6 C C3 AKG . . . E 5 17.067 -25.852 1.9 1 47.68 ? C3 AKG 262 A 1 HETATM 7 C C4 AKG . . . E 5 18.254 -25.04 1.404 1 46.99 ? C4 AKG 262 A 1 HETATM 8 C C5 AKG . . . E 5 18.713 -25.521 0.048 1 46.72 ? C5 AKG 262 A 1 HETATM 9 O O3 AKG . . . E 5 17.873 -25.965 -0.768 1 45.82 ? O3 AKG 262 A 1 HETATM 10 O O4 AKG . . . E 5 19.935 -25.452 -0.205 1 46.22 ? O4 AKG 262 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #