data_6YYW # _model_server_result.job_id VeZwMr2gDXdRz5vRaEaEqA _model_server_result.datetime_utc '2024-11-22 13:30:19' _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 6yyw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":802}' # _entry.id 6YYW # _exptl.entry_id 6YYW _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 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 6YYW _cell.length_a 50.439 _cell.length_b 90.951 _cell.length_c 123.605 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YYW _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 4 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 312 A CYS 641 1_555 A SG CYS 319 A CYS 648 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 B SG CYS 16 B CYS 101 1_555 B SG CYS 25 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc1 A NE2 HIS 350 A HIS 679 1_555 C MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc2 A NE2 HIS 396 A HIS 725 1_555 C MN MN . A MN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc3 C MN MN . A MN 801 1_555 D O5 AKG . A AKG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc4 C MN MN . A MN 801 1_555 D O2 AKG . A AKG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc5 C MN MN . A MN 801 1_555 E O HOH . A HOH 917 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc6 C MN MN . A MN 801 1_555 B OD2 ASP 18 B ASP 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? # _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 6YYW _atom_sites.fract_transf_matrix[1][1] 0.019826 _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] 0.010995 _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] 0.00809 _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 3 MN A 1 801 801 MN MN . D 4 AKG A 1 802 901 AKG AKG . E 5 HOH A 1 901 37 HOH HOH . E 5 HOH A 2 902 105 HOH HOH . E 5 HOH A 3 903 57 HOH HOH . E 5 HOH A 4 904 75 HOH HOH . E 5 HOH A 5 905 29 HOH HOH . E 5 HOH A 6 906 2 HOH HOH . E 5 HOH A 7 907 33 HOH HOH . E 5 HOH A 8 908 144 HOH HOH . E 5 HOH A 9 909 18 HOH HOH . E 5 HOH A 10 910 42 HOH HOH . E 5 HOH A 11 911 35 HOH HOH . E 5 HOH A 12 912 12 HOH HOH . E 5 HOH A 13 913 1 HOH HOH . E 5 HOH A 14 914 7 HOH HOH . E 5 HOH A 15 915 21 HOH HOH . E 5 HOH A 16 916 34 HOH HOH . E 5 HOH A 17 917 90 HOH HOH . E 5 HOH A 18 918 30 HOH HOH . E 5 HOH A 19 919 53 HOH HOH . E 5 HOH A 20 920 137 HOH HOH . E 5 HOH A 21 921 115 HOH HOH . E 5 HOH A 22 922 102 HOH HOH . E 5 HOH A 23 923 68 HOH HOH . E 5 HOH A 24 924 78 HOH HOH . E 5 HOH A 25 925 27 HOH HOH . E 5 HOH A 26 926 66 HOH HOH . E 5 HOH A 27 927 124 HOH HOH . E 5 HOH A 28 928 4 HOH HOH . E 5 HOH A 29 929 118 HOH HOH . E 5 HOH A 30 930 5 HOH HOH . E 5 HOH A 31 931 112 HOH HOH . E 5 HOH A 32 932 111 HOH HOH . E 5 HOH A 33 933 19 HOH HOH . E 5 HOH A 34 934 89 HOH HOH . E 5 HOH A 35 935 16 HOH HOH . E 5 HOH A 36 936 46 HOH HOH . E 5 HOH A 37 937 104 HOH HOH . E 5 HOH A 38 938 13 HOH HOH . E 5 HOH A 39 939 25 HOH HOH . E 5 HOH A 40 940 88 HOH HOH . E 5 HOH A 41 941 132 HOH HOH . E 5 HOH A 42 942 55 HOH HOH . E 5 HOH A 43 943 151 HOH HOH . E 5 HOH A 44 944 44 HOH HOH . E 5 HOH A 45 945 47 HOH HOH . E 5 HOH A 46 946 6 HOH HOH . E 5 HOH A 47 947 9 HOH HOH . E 5 HOH A 48 948 17 HOH HOH . E 5 HOH A 49 949 70 HOH HOH . E 5 HOH A 50 950 11 HOH HOH . E 5 HOH A 51 951 49 HOH HOH . E 5 HOH A 52 952 143 HOH HOH . E 5 HOH A 53 953 149 HOH HOH . E 5 HOH A 54 954 31 HOH HOH . E 5 HOH A 55 955 41 HOH HOH . E 5 HOH A 56 956 56 HOH HOH . E 5 HOH A 57 957 48 HOH HOH . E 5 HOH A 58 958 32 HOH HOH . E 5 HOH A 59 959 14 HOH HOH . E 5 HOH A 60 960 94 HOH HOH . E 5 HOH A 61 961 148 HOH HOH . E 5 HOH A 62 962 64 HOH HOH . E 5 HOH A 63 963 135 HOH HOH . E 5 HOH A 64 964 51 HOH HOH . E 5 HOH A 65 965 54 HOH HOH . E 5 HOH A 66 966 52 HOH HOH . E 5 HOH A 67 967 101 HOH HOH . E 5 HOH A 68 968 72 HOH HOH . E 5 HOH A 69 969 38 HOH HOH . E 5 HOH A 70 970 23 HOH HOH . E 5 HOH A 71 971 150 HOH HOH . E 5 HOH A 72 972 76 HOH HOH . E 5 HOH A 73 973 20 HOH HOH . E 5 HOH A 74 974 3 HOH HOH . E 5 HOH A 75 975 121 HOH HOH . E 5 HOH A 76 976 147 HOH HOH . E 5 HOH A 77 977 8 HOH HOH . E 5 HOH A 78 978 58 HOH HOH . E 5 HOH A 79 979 152 HOH HOH . E 5 HOH A 80 980 74 HOH HOH . E 5 HOH A 81 981 140 HOH HOH . E 5 HOH A 82 982 97 HOH HOH . E 5 HOH A 83 983 120 HOH HOH . E 5 HOH A 84 984 60 HOH HOH . E 5 HOH A 85 985 15 HOH HOH . E 5 HOH A 86 986 122 HOH HOH . E 5 HOH A 87 987 127 HOH HOH . E 5 HOH A 88 988 113 HOH HOH . E 5 HOH A 89 989 133 HOH HOH . E 5 HOH A 90 990 77 HOH HOH . E 5 HOH A 91 991 136 HOH HOH . E 5 HOH A 92 992 98 HOH HOH . E 5 HOH A 93 993 28 HOH HOH . E 5 HOH A 94 994 67 HOH HOH . E 5 HOH A 95 995 62 HOH HOH . E 5 HOH A 96 996 45 HOH HOH . E 5 HOH A 97 997 96 HOH HOH . E 5 HOH A 98 998 61 HOH HOH . E 5 HOH A 99 999 10 HOH HOH . E 5 HOH A 100 1000 43 HOH HOH . E 5 HOH A 101 1001 80 HOH HOH . E 5 HOH A 102 1002 116 HOH HOH . E 5 HOH A 103 1003 100 HOH HOH . E 5 HOH A 104 1004 145 HOH HOH . E 5 HOH A 105 1005 146 HOH HOH . E 5 HOH A 106 1006 141 HOH HOH . E 5 HOH A 107 1007 108 HOH HOH . E 5 HOH A 108 1008 131 HOH HOH . E 5 HOH A 109 1009 91 HOH HOH . E 5 HOH A 110 1010 63 HOH HOH . E 5 HOH A 111 1011 93 HOH HOH . E 5 HOH A 112 1012 65 HOH HOH . E 5 HOH A 113 1013 142 HOH HOH . E 5 HOH A 114 1014 103 HOH HOH . E 5 HOH A 115 1015 125 HOH HOH . E 5 HOH A 116 1016 110 HOH HOH . E 5 HOH A 117 1017 128 HOH HOH . E 5 HOH A 118 1018 24 HOH HOH . E 5 HOH A 119 1019 92 HOH HOH . E 5 HOH A 120 1020 129 HOH HOH . E 5 HOH A 121 1021 139 HOH HOH . E 5 HOH A 122 1022 107 HOH HOH . E 5 HOH A 123 1023 71 HOH HOH . E 5 HOH A 124 1024 59 HOH HOH . E 5 HOH A 125 1025 84 HOH HOH . E 5 HOH A 126 1026 82 HOH HOH . E 5 HOH A 127 1027 69 HOH HOH . E 5 HOH A 128 1028 134 HOH HOH . E 5 HOH A 129 1029 26 HOH HOH . E 5 HOH A 130 1030 99 HOH HOH . E 5 HOH A 131 1031 109 HOH HOH . E 5 HOH A 132 1032 117 HOH HOH . E 5 HOH A 133 1033 138 HOH HOH . E 5 HOH A 134 1034 126 HOH HOH . F 5 HOH B 1 201 114 HOH HOH . F 5 HOH B 2 202 106 HOH HOH . F 5 HOH B 3 203 130 HOH HOH . F 5 HOH B 4 204 39 HOH HOH . F 5 HOH B 5 205 86 HOH HOH . F 5 HOH B 6 206 83 HOH HOH . F 5 HOH B 7 207 85 HOH HOH . F 5 HOH B 8 208 87 HOH HOH . F 5 HOH B 9 209 119 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 . . . D 4 57.815 17.54 16.623 1 44.15 ? C1 AKG 802 A 1 HETATM 2 O O1 AKG . . . D 4 56.987 17.73 15.701 1 46.17 ? O1 AKG 802 A 1 HETATM 3 O O2 AKG . . . D 4 57.662 17.611 17.868 1 46.87 ? O2 AKG 802 A 1 HETATM 4 C C2 AKG . . . D 4 59.112 17.227 16.031 1 43.11 ? C2 AKG 802 A 1 HETATM 5 O O5 AKG . . . D 4 59.994 16.704 16.628 1 41.83 ? O5 AKG 802 A 1 HETATM 6 C C3 AKG . . . D 4 58.887 17.654 14.557 1 39 ? C3 AKG 802 A 1 HETATM 7 C C4 AKG . . . D 4 59.909 17.303 13.512 1 35.03 ? C4 AKG 802 A 1 HETATM 8 C C5 AKG . . . D 4 59.811 17.494 12.029 1 48.19 ? C5 AKG 802 A 1 HETATM 9 O O3 AKG . . . D 4 59.822 16.421 11.445 1 38.26 ? O3 AKG 802 A 1 HETATM 10 O O4 AKG . . . D 4 59.764 18.585 11.5 1 37.6 ? O4 AKG 802 A 1 HETATM 11 H H31 AKG . . . D 4 58.794 18.735 14.555 1 46.79 ? H31 AKG 802 A 1 HETATM 12 H H32 AKG . . . D 4 57.949 17.21 14.242 1 46.79 ? H32 AKG 802 A 1 HETATM 13 H H41 AKG . . . D 4 60.08 16.239 13.642 1 42.04 ? H41 AKG 802 A 1 HETATM 14 H H42 AKG . . . D 4 60.799 17.851 13.802 1 42.04 ? H42 AKG 802 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #