data_3U78 # _model_server_result.job_id ePdY9I0EpcXYjtmOI9pwlg _model_server_result.datetime_utc '2024-10-19 16:34:44' _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 3u78 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 3U78 # _exptl.entry_id 3U78 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.098 _entity.id 2 _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 3U78 _cell.length_a 77.429 _cell.length_b 77.429 _cell.length_c 289.685 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U78 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 2 _struct_asym.id B _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 NE2 HIS 191 A HIS 282 1_555 C NI NI . A NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc2 A OD1 ASP 193 A ASP 284 1_555 C NI NI . A NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc3 A NE2 HIS 263 A HIS 354 1_555 C NI NI . A NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc4 B O5 AKG . A AKG 701 1_555 C NI NI . A NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc5 B O1 AKG . A AKG 701 1_555 C NI NI . A NI 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc6 C NI NI . A NI 702 1_555 I O HOH . A HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? # _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 3U78 _atom_sites.fract_transf_matrix[1][1] 0.012915 _atom_sites.fract_transf_matrix[1][2] 0.007457 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014913 _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] 0.003452 _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 AKG A 1 701 701 AKG AKG . C 3 NI A 1 702 702 NI NI . D 4 CL A 1 703 703 CL CL . E 5 SO4 A 1 704 704 SO4 SO4 . F 6 EDO A 1 705 705 EDO EDO . G 6 EDO A 1 706 706 EDO EDO . H 7 E67 A 1 707 707 E67 E67 . I 8 HOH A 1 801 801 HOH HOH . I 8 HOH A 2 802 802 HOH HOH . I 8 HOH A 3 804 804 HOH HOH . I 8 HOH A 4 809 809 HOH HOH . I 8 HOH A 5 810 810 HOH HOH . I 8 HOH A 6 811 811 HOH HOH . I 8 HOH A 7 818 818 HOH HOH . I 8 HOH A 8 821 821 HOH HOH . I 8 HOH A 9 823 823 HOH HOH . I 8 HOH A 10 824 824 HOH HOH . I 8 HOH A 11 826 826 HOH HOH . I 8 HOH A 12 829 829 HOH HOH . I 8 HOH A 13 831 831 HOH HOH . I 8 HOH A 14 832 832 HOH HOH . I 8 HOH A 15 833 833 HOH HOH . I 8 HOH A 16 834 834 HOH HOH . I 8 HOH A 17 835 835 HOH HOH . I 8 HOH A 18 836 836 HOH HOH . I 8 HOH A 19 837 837 HOH HOH . I 8 HOH A 20 838 838 HOH HOH . I 8 HOH A 21 840 840 HOH HOH . I 8 HOH A 22 842 842 HOH HOH . I 8 HOH A 23 843 843 HOH HOH . I 8 HOH A 24 844 844 HOH HOH . I 8 HOH A 25 846 846 HOH HOH . I 8 HOH A 26 848 848 HOH HOH . I 8 HOH A 27 855 855 HOH HOH . I 8 HOH A 28 856 856 HOH HOH . I 8 HOH A 29 857 857 HOH HOH . I 8 HOH A 30 859 859 HOH HOH . I 8 HOH A 31 861 861 HOH HOH . I 8 HOH A 32 863 863 HOH HOH . I 8 HOH A 33 864 864 HOH HOH . I 8 HOH A 34 865 865 HOH HOH . I 8 HOH A 35 866 866 HOH HOH . I 8 HOH A 36 867 867 HOH HOH . I 8 HOH A 37 868 868 HOH HOH . I 8 HOH A 38 869 869 HOH HOH . I 8 HOH A 39 870 870 HOH HOH . I 8 HOH A 40 871 871 HOH HOH . I 8 HOH A 41 872 872 HOH HOH . I 8 HOH A 42 873 873 HOH HOH . I 8 HOH A 43 874 874 HOH HOH . I 8 HOH A 44 876 876 HOH HOH . I 8 HOH A 45 877 877 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 . . . B 2 -41.331 22.77 9.718 1 46.08 ? C1 AKG 701 A 1 HETATM 2 O O1 AKG . . . B 2 -40.856 23.85 10.172 1 42.23 ? O1 AKG 701 A 1 HETATM 3 O O2 AKG . . . B 2 -40.93 21.677 10.209 1 44.82 ? O2 AKG 701 A 1 HETATM 4 C C2 AKG . . . B 2 -42.372 22.757 8.63 1 46.1 ? C2 AKG 701 A 1 HETATM 5 O O5 AKG . . . B 2 -43.17 23.687 8.514 1 39.56 ? O5 AKG 701 A 1 HETATM 6 C C3 AKG . . . B 2 -42.726 21.445 8.004 1 39.03 ? C3 AKG 701 A 1 HETATM 7 C C4 AKG . . . B 2 -43.733 20.796 8.895 1 38.11 ? C4 AKG 701 A 1 HETATM 8 C C5 AKG . . . B 2 -44.151 19.451 8.39 1 38.92 ? C5 AKG 701 A 1 HETATM 9 O O3 AKG . . . B 2 -43.886 19.092 7.214 1 36.85 ? O3 AKG 701 A 1 HETATM 10 O O4 AKG . . . B 2 -44.88 18.713 9.111 1 39.14 ? O4 AKG 701 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #