data_8JPW # _model_server_result.job_id GDT3eGymuxA2us11EqLnmA _model_server_result.datetime_utc '2025-04-25 19:45:05' _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 8jpw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 8JPW # _exptl.entry_id 8JPW _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 90 _cell.entry_id 8JPW _cell.length_a 158.4 _cell.length_b 158.4 _cell.length_c 138.235 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JPW _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _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 OD1 ASP 167 A ASP 167 1_555 E ZN ZN . A ZN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc2 A OE1 GLU 346 A GLU 346 1_555 D ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc3 A OE2 GLU 475 A GLU 465 1_555 E ZN ZN . A ZN 703 15_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? # _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 8JPW _atom_sites.fract_transf_matrix[1][1] 0.006313 _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] 0.006313 _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] 0.007234 _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 FAD A 1 700 700 FAD FAD . C 3 AKG A 1 701 701 AKG AKZ . D 4 ZN A 1 702 702 ZN ZN . E 4 ZN A 1 703 703 ZN ZN . F 5 HOH A 1 801 885 HOH HOH . F 5 HOH A 2 802 793 HOH HOH . F 5 HOH A 3 803 875 HOH HOH . F 5 HOH A 4 804 833 HOH HOH . F 5 HOH A 5 805 841 HOH HOH . F 5 HOH A 6 806 861 HOH HOH . F 5 HOH A 7 807 882 HOH HOH . F 5 HOH A 8 808 766 HOH HOH . F 5 HOH A 9 809 845 HOH HOH . F 5 HOH A 10 810 857 HOH HOH . F 5 HOH A 11 811 853 HOH HOH . F 5 HOH A 12 812 798 HOH HOH . F 5 HOH A 13 813 881 HOH HOH . F 5 HOH A 14 814 829 HOH HOH . F 5 HOH A 15 815 731 HOH HOH . F 5 HOH A 16 816 788 HOH HOH . F 5 HOH A 17 817 740 HOH HOH . F 5 HOH A 18 818 775 HOH HOH . F 5 HOH A 19 819 849 HOH HOH . F 5 HOH A 20 820 889 HOH HOH . F 5 HOH A 21 821 781 HOH HOH . F 5 HOH A 22 822 869 HOH HOH . F 5 HOH A 23 823 855 HOH HOH . F 5 HOH A 24 824 726 HOH HOH . F 5 HOH A 25 825 824 HOH HOH . F 5 HOH A 26 826 733 HOH HOH . F 5 HOH A 27 827 838 HOH HOH . F 5 HOH A 28 828 864 HOH HOH . F 5 HOH A 29 829 854 HOH HOH . F 5 HOH A 30 830 893 HOH HOH . F 5 HOH A 31 831 887 HOH HOH . F 5 HOH A 32 832 724 HOH HOH . F 5 HOH A 33 833 865 HOH HOH . F 5 HOH A 34 834 754 HOH HOH . F 5 HOH A 35 835 716 HOH HOH . F 5 HOH A 36 836 748 HOH HOH . F 5 HOH A 37 837 866 HOH HOH . F 5 HOH A 38 838 863 HOH HOH . F 5 HOH A 39 839 732 HOH HOH . F 5 HOH A 40 840 722 HOH HOH . F 5 HOH A 41 841 867 HOH HOH . F 5 HOH A 42 842 723 HOH HOH . F 5 HOH A 43 843 813 HOH HOH . F 5 HOH A 44 844 815 HOH HOH . F 5 HOH A 45 845 886 HOH HOH . F 5 HOH A 46 846 768 HOH HOH . F 5 HOH A 47 847 734 HOH HOH . F 5 HOH A 48 848 856 HOH HOH . F 5 HOH A 49 849 714 HOH HOH . F 5 HOH A 50 850 874 HOH HOH . F 5 HOH A 51 851 818 HOH HOH . F 5 HOH A 52 852 837 HOH HOH . F 5 HOH A 53 853 873 HOH HOH . F 5 HOH A 54 854 892 HOH HOH . F 5 HOH A 55 855 891 HOH HOH . F 5 HOH A 56 856 860 HOH HOH . F 5 HOH A 57 857 747 HOH HOH . F 5 HOH A 58 858 710 HOH HOH . F 5 HOH A 59 859 777 HOH HOH . F 5 HOH A 60 860 852 HOH HOH . F 5 HOH A 61 861 749 HOH HOH . F 5 HOH A 62 862 878 HOH HOH . F 5 HOH A 63 863 770 HOH HOH . F 5 HOH A 64 864 759 HOH HOH . F 5 HOH A 65 865 783 HOH HOH . F 5 HOH A 66 866 851 HOH HOH . F 5 HOH A 67 867 745 HOH HOH . F 5 HOH A 68 868 862 HOH HOH . F 5 HOH A 69 869 847 HOH HOH . F 5 HOH A 70 870 765 HOH HOH . F 5 HOH A 71 871 796 HOH HOH . F 5 HOH A 72 872 868 HOH HOH . F 5 HOH A 73 873 825 HOH HOH . F 5 HOH A 74 874 750 HOH HOH . F 5 HOH A 75 875 817 HOH HOH . F 5 HOH A 76 876 718 HOH HOH . F 5 HOH A 77 877 820 HOH HOH . F 5 HOH A 78 878 784 HOH HOH . F 5 HOH A 79 879 736 HOH HOH . F 5 HOH A 80 880 717 HOH HOH . F 5 HOH A 81 881 725 HOH HOH . F 5 HOH A 82 882 840 HOH HOH . F 5 HOH A 83 883 884 HOH HOH . F 5 HOH A 84 884 795 HOH HOH . F 5 HOH A 85 885 719 HOH HOH . F 5 HOH A 86 886 738 HOH HOH . F 5 HOH A 87 887 809 HOH HOH . F 5 HOH A 88 888 760 HOH HOH . F 5 HOH A 89 889 730 HOH HOH . F 5 HOH A 90 890 735 HOH HOH . F 5 HOH A 91 891 883 HOH HOH . F 5 HOH A 92 892 728 HOH HOH . F 5 HOH A 93 893 823 HOH HOH . F 5 HOH A 94 894 715 HOH HOH . F 5 HOH A 95 895 839 HOH HOH . F 5 HOH A 96 896 764 HOH HOH . F 5 HOH A 97 897 757 HOH HOH . F 5 HOH A 98 898 805 HOH HOH . F 5 HOH A 99 899 756 HOH HOH . F 5 HOH A 100 900 834 HOH HOH . F 5 HOH A 101 901 802 HOH HOH . F 5 HOH A 102 902 826 HOH HOH . F 5 HOH A 103 903 752 HOH HOH . F 5 HOH A 104 904 743 HOH HOH . F 5 HOH A 105 905 801 HOH HOH . F 5 HOH A 106 906 727 HOH HOH . F 5 HOH A 107 907 790 HOH HOH . F 5 HOH A 108 908 871 HOH HOH . F 5 HOH A 109 909 755 HOH HOH . F 5 HOH A 110 910 712 HOH HOH . F 5 HOH A 111 911 794 HOH HOH . F 5 HOH A 112 912 786 HOH HOH . F 5 HOH A 113 913 814 HOH HOH . F 5 HOH A 114 914 877 HOH HOH . F 5 HOH A 115 915 850 HOH HOH . F 5 HOH A 116 916 761 HOH HOH . F 5 HOH A 117 917 774 HOH HOH . F 5 HOH A 118 918 789 HOH HOH . F 5 HOH A 119 919 767 HOH HOH . F 5 HOH A 120 920 800 HOH HOH . F 5 HOH A 121 921 836 HOH HOH . F 5 HOH A 122 922 741 HOH HOH . F 5 HOH A 123 923 880 HOH HOH . F 5 HOH A 124 924 797 HOH HOH . F 5 HOH A 125 925 776 HOH HOH . F 5 HOH A 126 926 890 HOH HOH . F 5 HOH A 127 927 739 HOH HOH . F 5 HOH A 128 928 835 HOH HOH . F 5 HOH A 129 929 872 HOH HOH . F 5 HOH A 130 930 751 HOH HOH . F 5 HOH A 131 931 737 HOH HOH . F 5 HOH A 132 932 821 HOH HOH . F 5 HOH A 133 933 769 HOH HOH . F 5 HOH A 134 934 779 HOH HOH . F 5 HOH A 135 935 792 HOH HOH . F 5 HOH A 136 936 753 HOH HOH . F 5 HOH A 137 937 807 HOH HOH . F 5 HOH A 138 938 721 HOH HOH . F 5 HOH A 139 939 744 HOH HOH . F 5 HOH A 140 940 758 HOH HOH . F 5 HOH A 141 941 832 HOH HOH . F 5 HOH A 142 942 831 HOH HOH . F 5 HOH A 143 943 844 HOH HOH . F 5 HOH A 144 944 742 HOH HOH . F 5 HOH A 145 945 870 HOH HOH . F 5 HOH A 146 946 729 HOH HOH . F 5 HOH A 147 947 808 HOH HOH . F 5 HOH A 148 948 812 HOH HOH . F 5 HOH A 149 949 782 HOH HOH . F 5 HOH A 150 950 711 HOH HOH . F 5 HOH A 151 951 816 HOH HOH . F 5 HOH A 152 952 763 HOH HOH . F 5 HOH A 153 953 828 HOH HOH . F 5 HOH A 154 954 772 HOH HOH . F 5 HOH A 155 955 713 HOH HOH . F 5 HOH A 156 956 785 HOH HOH . F 5 HOH A 157 957 848 HOH HOH . F 5 HOH A 158 958 819 HOH HOH . F 5 HOH A 159 959 879 HOH HOH . F 5 HOH A 160 960 803 HOH HOH . F 5 HOH A 161 961 773 HOH HOH . F 5 HOH A 162 962 778 HOH HOH . F 5 HOH A 163 963 720 HOH HOH . F 5 HOH A 164 964 859 HOH HOH . F 5 HOH A 165 965 858 HOH HOH . F 5 HOH A 166 966 846 HOH HOH . F 5 HOH A 167 967 888 HOH HOH . F 5 HOH A 168 968 780 HOH HOH . F 5 HOH A 169 969 806 HOH HOH . F 5 HOH A 170 970 804 HOH HOH . F 5 HOH A 171 971 843 HOH HOH . F 5 HOH A 172 972 799 HOH HOH . F 5 HOH A 173 973 830 HOH HOH . F 5 HOH A 174 974 746 HOH HOH . F 5 HOH A 175 975 822 HOH HOH . F 5 HOH A 176 976 810 HOH HOH . F 5 HOH A 177 977 876 HOH HOH . F 5 HOH A 178 978 811 HOH HOH . F 5 HOH A 179 979 791 HOH HOH . F 5 HOH A 180 980 762 HOH HOH . F 5 HOH A 181 981 787 HOH HOH . F 5 HOH A 182 982 827 HOH HOH . F 5 HOH A 183 983 842 HOH HOH . F 5 HOH A 184 984 771 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 -3.537 41.851 17.393 1 87.04 ? C1 AKG 701 A 1 HETATM 2 O O1 AKG . . . C 3 -2.64 40.964 17.456 1 79.61 ? O1 AKG 701 A 1 HETATM 3 O O2 AKG . . . C 3 -4.529 41.805 18.152 1 85.02 ? O2 AKG 701 A 1 HETATM 4 C C2 AKG . . . C 3 -3.508 42.976 16.435 1 86 ? C2 AKG 701 A 1 HETATM 5 O O5 AKG . . . C 3 -2.664 43.099 15.544 1 74.75 ? O5 AKG 701 A 1 HETATM 6 C C3 AKG . . . C 3 -4.607 44.006 16.581 1 87.92 ? C3 AKG 701 A 1 HETATM 7 C C4 AKG . . . C 3 -5.954 43.408 16.156 1 90.71 ? C4 AKG 701 A 1 HETATM 8 C C5 AKG . . . C 3 -7.106 43.697 17.11 1 82.03 ? C5 AKG 701 A 1 HETATM 9 O O3 AKG . . . C 3 -8.126 42.987 16.957 1 75.49 ? O3 AKG 701 A 1 HETATM 10 O O4 AKG . . . C 3 -7.041 44.622 17.967 1 72.14 ? O4 AKG 701 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 10 #