data_6D3J # _model_server_result.job_id nn1aNSNmqZyTXXvCCAWyGA _model_server_result.datetime_utc '2024-11-01 13:30:05' _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 6d3j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6D3J # _exptl.entry_id 6D3J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 3 _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 6D3J _cell.length_a 137.413 _cell.length_b 137.413 _cell.length_c 76.261 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D3J _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 68.7065 -119.003149 0 3 'crystal symmetry operation' 9_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 25.420333 4 'crystal symmetry operation' 12_545 x,x-y-1,-z+1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 68.7065 -119.003149 25.420333 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 A OD2 ASP 16 A ASP 16 1_555 D CO CO . A CO 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc2 A OE1 GLU 35 A GLU 35 1_555 E CO CO . A CO 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc3 A OD2 ASP 108 A ASP 108 1_555 L CO CO . A CO 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc4 A NE2 HIS 111 A HIS 111 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc5 A OD2 ASP 113 A ASP 113 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc6 A OD1 ASP 118 A ASP 118 1_555 H CO CO . A CO 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc7 A OE2 GLU 242 A GLU 242 1_555 J CO CO . A CO 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc8 A OE2 GLU 242 A GLU 242 1_555 M CO CO . A CO 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc9 A NE2 HIS 270 A HIS 270 1_555 B CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc10 B CO CO . A CO 301 1_555 C C2 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc11 B CO CO . A CO 301 1_555 C O5 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc12 B CO CO . A CO 301 1_555 C C1 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc13 B CO CO . A CO 301 1_555 O O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? # _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 6D3J _atom_sites.fract_transf_matrix[1][1] 0.007277 _atom_sites.fract_transf_matrix[1][2] 0.004202 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008403 _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] 0.013113 _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 CO A 1 301 1 CO CO . C 3 AKG A 1 302 3 AKG AKG . D 2 CO A 1 303 1 CO CO . E 2 CO A 1 304 2 CO CO . F 2 CO A 1 305 3 CO CO . G 2 CO A 1 306 4 CO CO . H 2 CO A 1 307 5 CO CO . I 2 CO A 1 308 6 CO CO . J 2 CO A 1 309 7 CO CO . K 2 CO A 1 310 1 CO CO . L 2 CO A 1 311 2 CO CO . M 2 CO A 1 312 3 CO CO . N 2 CO A 1 313 4 CO CO . O 4 HOH A 1 401 1 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 . . . C 3 27.527 -37.014 -3.477 1 144.35 ? C1 AKG 302 A 1 HETATM 2 O O1 AKG . . . C 3 27.189 -36.577 -4.61 1 151.8 ? O1 AKG 302 A 1 HETATM 3 O O2 AKG . . . C 3 28.677 -36.78 -3.055 1 161.23 ? O2 AKG 302 A 1 HETATM 4 C C2 AKG . . . C 3 26.683 -37.892 -2.634 1 131.61 ? C2 AKG 302 A 1 HETATM 5 O O5 AKG . . . C 3 26.986 -39.073 -2.633 1 139.52 ? O5 AKG 302 A 1 HETATM 6 C C3 AKG . . . C 3 25.508 -37.495 -1.75 1 123.95 ? C3 AKG 302 A 1 HETATM 7 C C4 AKG . . . C 3 24.935 -36.075 -1.848 1 121.88 ? C4 AKG 302 A 1 HETATM 8 C C5 AKG . . . C 3 23.446 -36.3 -2.052 1 131.73 ? C5 AKG 302 A 1 HETATM 9 O O3 AKG . . . C 3 23.079 -36.625 -3.212 1 135.42 ? O3 AKG 302 A 1 HETATM 10 O O4 AKG . . . C 3 22.636 -36.219 -1.078 1 144.65 ? O4 AKG 302 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #