data_1GY9 # _model_server_result.job_id 5wHtPWJKPesL8bE5GShsig _model_server_result.datetime_utc '2024-11-24 22:49:39' _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 1gy9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":351}' # _entry.id 1GY9 # _exptl.entry_id 1GY9 _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 2 _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 1GY9 _cell.length_a 116.786 _cell.length_b 116.786 _cell.length_c 201.937 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GY9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 62 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,G,H,I,K 1 1,2,3,4 A,C,D,E,F,J 2 1,5,6,7 # 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 116.786 0 0 3 'crystal symmetry operation' 8_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 201.937 4 'crystal symmetry operation' 11_656 -x+y+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 116.786 0 201.937 5 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 58.393 101.139643 0 6 'crystal symmetry operation' 7_555 y,x,-z+2/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 134.624667 7 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+2/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 58.393 101.139643 134.624667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 I 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 OE1 GLU 33 A GLU 33 12_555 D FE FE . A FE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc2 A OE1 GLU 33 A GLU 33 1_555 D FE FE . A FE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc3 A NE2 HIS 37 A HIS 37 1_555 D FE FE . A FE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc4 A NE2 HIS 37 A HIS 37 12_555 D FE FE . A FE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc5 A NE2 HIS 99 A HIS 99 1_555 C FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc6 A OD1 ASP 101 A ASP 101 1_555 C FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc7 A NE2 HIS 255 A HIS 255 1_555 C FE FE . A FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc8 C FE FE . A FE 300 1_555 F O1 AKG . A AKG 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc9 C FE FE . A FE 300 1_555 F O5 AKG . A AKG 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc10 B NE2 HIS 99 B HIS 99 1_555 G FE FE . B FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc11 B OD1 ASP 101 B ASP 101 1_555 G FE FE . B FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc12 B NE2 HIS 255 B HIS 255 1_555 G FE FE . B FE 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc13 G FE FE . B FE 300 1_555 I O5 AKG . B AKG 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc14 G FE FE . B FE 300 1_555 I O1 AKG . B AKG 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? # _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 1GY9 _atom_sites.fract_transf_matrix[1][1] 0.008563 _atom_sites.fract_transf_matrix[1][2] 0.004944 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009887 _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] 0.004952 _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 C 2 FE A 1 300 300 FE FE . D 2 FE A 1 310 310 FE FE . E 3 TAU A 1 350 350 TAU TAU . F 4 AKG A 1 351 351 AKG AKG . G 2 FE B 1 300 300 FE FE . H 3 TAU B 1 350 350 TAU TAU . I 4 AKG B 1 351 351 AKG AKG . J 5 HOH A 1 2001 2001 HOH HOH . J 5 HOH A 2 2002 2002 HOH HOH . J 5 HOH A 3 2003 2003 HOH HOH . J 5 HOH A 4 2004 2004 HOH HOH . J 5 HOH A 5 2005 2005 HOH HOH . J 5 HOH A 6 2006 2006 HOH HOH . J 5 HOH A 7 2007 2007 HOH HOH . J 5 HOH A 8 2008 2008 HOH HOH . J 5 HOH A 9 2009 2009 HOH HOH . J 5 HOH A 10 2010 2010 HOH HOH . J 5 HOH A 11 2011 2011 HOH HOH . J 5 HOH A 12 2012 2012 HOH HOH . J 5 HOH A 13 2013 2013 HOH HOH . J 5 HOH A 14 2014 2014 HOH HOH . J 5 HOH A 15 2015 2015 HOH HOH . J 5 HOH A 16 2016 2016 HOH HOH . J 5 HOH A 17 2017 2017 HOH HOH . J 5 HOH A 18 2018 2018 HOH HOH . K 5 HOH B 1 2001 2001 HOH HOH . K 5 HOH B 2 2002 2002 HOH HOH . K 5 HOH B 3 2003 2003 HOH HOH . K 5 HOH B 4 2004 2004 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 . . . I 4 55.28 16.678 77.935 1 25.11 ? C1 AKG 351 B 1 HETATM 2 O O1 AKG . . . I 4 54.28 16.741 78.557 1 23.13 ? O1 AKG 351 B 1 HETATM 3 O O2 AKG . . . I 4 55.509 17.38 76.829 1 28.87 ? O2 AKG 351 B 1 HETATM 4 C C2 AKG . . . I 4 56.313 15.732 78.445 1 23.61 ? C2 AKG 351 B 1 HETATM 5 O O5 AKG . . . I 4 56.058 15.146 79.437 1 24.7 ? O5 AKG 351 B 1 HETATM 6 C C3 AKG . . . I 4 57.573 15.605 77.636 1 25.39 ? C3 AKG 351 B 1 HETATM 7 C C4 AKG . . . I 4 57.354 14.558 76.536 1 25.21 ? C4 AKG 351 B 1 HETATM 8 C C5 AKG . . . I 4 58.657 14.455 75.779 1 26.93 ? C5 AKG 351 B 1 HETATM 9 O O3 AKG . . . I 4 59.464 15.364 75.902 1 29.78 ? O3 AKG 351 B 1 HETATM 10 O O4 AKG . . . I 4 58.936 13.428 74.988 1 25.73 ? O4 AKG 351 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #