data_6D3I # _model_server_result.job_id 6E5YnyetEgqLEn4q2zLvrw _model_server_result.datetime_utc '2024-11-24 08:45:16' _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 6d3i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":302}' # _entry.id 6D3I # _exptl.entry_id 6D3I _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 4 _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 6D3I _cell.length_a 94.927 _cell.length_b 109.98 _cell.length_c 116.145 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D3I _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,J,K,L,O,Q 1 1 B,D,G,H,I,M,N,P,R 1 2 # 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' 1_655 x+1,y,z 1 0 0 0 1 0 0 0 1 94.927 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 K N N ? 3 N N 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 NE2 HIS 111 A HIS 111 1_555 E CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc2 A OD1 ASP 113 A ASP 113 1_555 E CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc3 A NE2 HIS 270 A HIS 270 1_555 E CO CO . A CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc4 E CO CO . A CO 301 1_555 F O1 AKG . A AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc5 B NE2 HIS 111 G HIS 111 1_555 G CO CO . G CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc6 B OD1 ASP 113 G ASP 113 1_555 G CO CO . G CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc7 B NE2 HIS 270 G HIS 270 1_555 G CO CO . G CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.717 ? metalc ? metalc8 G CO CO . G CO 301 1_555 H O5 AKG . G AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc9 C NE2 HIS 111 D HIS 111 1_555 J CO CO . D CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc10 C OD1 ASP 113 D ASP 113 1_555 J CO CO . D CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc11 C NE2 HIS 270 D HIS 270 1_555 J CO CO . D CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? metalc ? metalc12 J CO CO . D CO 301 1_555 K O5 AKG . D AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc13 D NE2 HIS 111 J HIS 111 1_555 M CO CO . J CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc14 D OD1 ASP 113 J ASP 113 1_555 M CO CO . J CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? metalc ? metalc15 D NE2 HIS 270 J HIS 270 1_555 M CO CO . J CO 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc16 M CO CO . J CO 301 1_555 N O2 AKG . J AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? metalc ? metalc17 M CO CO . J CO 301 1_555 N O5 AKG . J AKG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? # _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 6D3I _atom_sites.fract_transf_matrix[1][1] 0.010534 _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] 0.009093 _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] 0.00861 _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 E 2 CO A 1 301 4 CO CO . F 3 AKG A 1 302 3 AKG AKG . G 2 CO G 1 301 1 CO CO . H 3 AKG G 1 302 4 AKG AKG . I 4 CFA G 1 303 701 CFA 24D . J 2 CO D 1 301 1 CO CO . K 3 AKG D 1 302 4 AKG AKG . L 4 CFA D 1 303 701 CFA 24D . M 2 CO J 1 301 1 CO CO . N 3 AKG J 1 302 4 AKG AKG . O 5 HOH A 1 401 13 HOH HOH . O 5 HOH A 2 402 48 HOH HOH . O 5 HOH A 3 403 20 HOH HOH . O 5 HOH A 4 404 55 HOH HOH . O 5 HOH A 5 405 29 HOH HOH . O 5 HOH A 6 406 63 HOH HOH . O 5 HOH A 7 407 40 HOH HOH . O 5 HOH A 8 408 10 HOH HOH . O 5 HOH A 9 409 70 HOH HOH . O 5 HOH A 10 410 31 HOH HOH . O 5 HOH A 11 411 1 HOH HOH . O 5 HOH A 12 412 18 HOH HOH . O 5 HOH A 13 413 3 HOH HOH . O 5 HOH A 14 414 46 HOH HOH . O 5 HOH A 15 415 50 HOH HOH . P 5 HOH G 1 401 15 HOH HOH . P 5 HOH G 2 402 41 HOH HOH . P 5 HOH G 3 403 2 HOH HOH . P 5 HOH G 4 404 14 HOH HOH . P 5 HOH G 5 405 66 HOH HOH . P 5 HOH G 6 406 67 HOH HOH . P 5 HOH G 7 407 56 HOH HOH . P 5 HOH G 8 408 44 HOH HOH . P 5 HOH G 9 409 59 HOH HOH . P 5 HOH G 10 410 32 HOH HOH . Q 5 HOH D 1 401 68 HOH HOH . Q 5 HOH D 2 402 6 HOH HOH . Q 5 HOH D 3 403 8 HOH HOH . Q 5 HOH D 4 404 7 HOH HOH . Q 5 HOH D 5 405 12 HOH HOH . Q 5 HOH D 6 406 51 HOH HOH . Q 5 HOH D 7 407 22 HOH HOH . Q 5 HOH D 8 408 16 HOH HOH . Q 5 HOH D 9 409 45 HOH HOH . R 5 HOH J 1 401 5 HOH HOH . R 5 HOH J 2 402 24 HOH HOH . R 5 HOH J 3 403 19 HOH HOH . R 5 HOH J 4 404 43 HOH HOH . R 5 HOH J 5 405 60 HOH HOH . R 5 HOH J 6 406 36 HOH HOH . R 5 HOH J 7 407 69 HOH HOH . R 5 HOH J 8 408 35 HOH HOH . R 5 HOH J 9 409 47 HOH HOH . R 5 HOH J 10 410 38 HOH HOH . R 5 HOH J 11 411 52 HOH HOH . R 5 HOH J 12 412 23 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 . . . K 3 2.628 13.632 3.648 1 44.83 ? C1 AKG 302 D 1 HETATM 2 O O1 AKG . . . K 3 1.722 14.004 2.871 1 44.58 ? O1 AKG 302 D 1 HETATM 3 O O2 AKG . . . K 3 3.239 14.474 4.349 1 44.77 ? O2 AKG 302 D 1 HETATM 4 C C2 AKG . . . K 3 3.009 12.157 3.745 1 56.82 ? C2 AKG 302 D 1 HETATM 5 O O5 AKG . . . K 3 3.951 11.868 4.413 1 58.09 ? O5 AKG 302 D 1 HETATM 6 C C3 AKG . . . K 3 2.247 11.069 2.968 1 48.93 ? C3 AKG 302 D 1 HETATM 7 C C4 AKG . . . K 3 1.005 10.589 3.703 1 38.33 ? C4 AKG 302 D 1 HETATM 8 C C5 AKG . . . K 3 0.171 9.737 2.75 1 49.18 ? C5 AKG 302 D 1 HETATM 9 O O3 AKG . . . K 3 0.363 9.815 1.503 1 49.19 ? O3 AKG 302 D 1 HETATM 10 O O4 AKG . . . K 3 -0.703 8.952 3.219 1 50.34 ? O4 AKG 302 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #