data_6PDD # _model_server_result.job_id 6-o9P5_2nJkSwBQvYkSI7A _model_server_result.datetime_utc '2024-11-29 10:31:32' _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 6pdd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":805}' # _entry.id 6PDD # _exptl.entry_id 6PDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 90 _cell.entry_id 6PDD _cell.length_a 46.177 _cell.length_b 57.005 _cell.length_c 122.186 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PDD _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F 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 covale ? covale1 A C HIS 97 A HIS 603 1_555 A N ALY 98 A ALY 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C ALY 98 A ALY 604 1_555 A N THR 99 A THR 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? metalc ? metalc1 A SG CYS 34 A CYS 540 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc2 A SG CYS 37 A CYS 543 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc3 A NE2 HIS 50 A HIS 556 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc4 A SG CYS 54 A CYS 560 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 C NA NA . A NA 802 1_555 H O HOH . A HOH 924 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.087 ? metalc ? metalc6 C NA NA . A NA 802 1_555 H O HOH . A HOH 938 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.078 ? metalc ? metalc7 C NA NA . A NA 802 1_555 H O HOH . A HOH 1028 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 GOL sing 157 n n C1 C2 GOL sing 158 n n C1 H11 GOL sing 159 n n C1 H12 GOL sing 160 n n O1 HO1 GOL sing 161 n n C2 O2 GOL sing 162 n n C2 C3 GOL sing 163 n n C2 H2 GOL sing 164 n n O2 HO2 GOL sing 165 n n C3 O3 GOL sing 166 n n C3 H31 GOL sing 167 n n C3 H32 GOL sing 168 n n O3 HO3 GOL sing 169 n n # _atom_sites.entry_id 6PDD _atom_sites.fract_transf_matrix[1][1] 0.021656 _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] 0.017542 _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] 0.008184 _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 ZN A 1 801 506 ZN ZN . C 3 NA A 1 802 507 NA NA . D 4 O9S A 1 803 1 O9S LIG . E 5 GOL A 1 804 1 GOL GOL . F 5 GOL A 1 805 2 GOL GOL . G 6 SO4 A 1 806 3 SO4 SO4 . H 7 HOH A 1 901 34 HOH HOH . H 7 HOH A 2 902 148 HOH HOH . H 7 HOH A 3 903 151 HOH HOH . H 7 HOH A 4 904 87 HOH HOH . H 7 HOH A 5 905 173 HOH HOH . H 7 HOH A 6 906 4 HOH HOH . H 7 HOH A 7 907 141 HOH HOH . H 7 HOH A 8 908 184 HOH HOH . H 7 HOH A 9 909 122 HOH HOH . H 7 HOH A 10 910 150 HOH HOH . H 7 HOH A 11 911 57 HOH HOH . H 7 HOH A 12 912 12 HOH HOH . H 7 HOH A 13 913 186 HOH HOH . H 7 HOH A 14 914 131 HOH HOH . H 7 HOH A 15 915 20 HOH HOH . H 7 HOH A 16 916 1 HOH HOH . H 7 HOH A 17 917 45 HOH HOH . H 7 HOH A 18 918 89 HOH HOH . H 7 HOH A 19 919 191 HOH HOH . H 7 HOH A 20 920 67 HOH HOH . H 7 HOH A 21 921 200 HOH HOH . H 7 HOH A 22 922 117 HOH HOH . H 7 HOH A 23 923 176 HOH HOH . H 7 HOH A 24 924 164 HOH HOH . H 7 HOH A 25 925 44 HOH HOH . H 7 HOH A 26 926 14 HOH HOH . H 7 HOH A 27 927 78 HOH HOH . H 7 HOH A 28 928 8 HOH HOH . H 7 HOH A 29 929 16 HOH HOH . H 7 HOH A 30 930 53 HOH HOH . H 7 HOH A 31 931 40 HOH HOH . H 7 HOH A 32 932 6 HOH HOH . H 7 HOH A 33 933 5 HOH HOH . H 7 HOH A 34 934 138 HOH HOH . H 7 HOH A 35 935 21 HOH HOH . H 7 HOH A 36 936 72 HOH HOH . H 7 HOH A 37 937 9 HOH HOH . H 7 HOH A 38 938 165 HOH HOH . H 7 HOH A 39 939 59 HOH HOH . H 7 HOH A 40 940 13 HOH HOH . H 7 HOH A 41 941 63 HOH HOH . H 7 HOH A 42 942 43 HOH HOH . H 7 HOH A 43 943 3 HOH HOH . H 7 HOH A 44 944 170 HOH HOH . H 7 HOH A 45 945 142 HOH HOH . H 7 HOH A 46 946 127 HOH HOH . H 7 HOH A 47 947 46 HOH HOH . H 7 HOH A 48 948 30 HOH HOH . H 7 HOH A 49 949 206 HOH HOH . H 7 HOH A 50 950 32 HOH HOH . H 7 HOH A 51 951 2 HOH HOH . H 7 HOH A 52 952 39 HOH HOH . H 7 HOH A 53 953 197 HOH HOH . H 7 HOH A 54 954 11 HOH HOH . H 7 HOH A 55 955 112 HOH HOH . H 7 HOH A 56 956 194 HOH HOH . H 7 HOH A 57 957 140 HOH HOH . H 7 HOH A 58 958 167 HOH HOH . H 7 HOH A 59 959 198 HOH HOH . H 7 HOH A 60 960 84 HOH HOH . H 7 HOH A 61 961 183 HOH HOH . H 7 HOH A 62 962 54 HOH HOH . H 7 HOH A 63 963 91 HOH HOH . H 7 HOH A 64 964 132 HOH HOH . H 7 HOH A 65 965 28 HOH HOH . H 7 HOH A 66 966 201 HOH HOH . H 7 HOH A 67 967 27 HOH HOH . H 7 HOH A 68 968 204 HOH HOH . H 7 HOH A 69 969 159 HOH HOH . H 7 HOH A 70 970 29 HOH HOH . H 7 HOH A 71 971 52 HOH HOH . H 7 HOH A 72 972 179 HOH HOH . H 7 HOH A 73 973 74 HOH HOH . H 7 HOH A 74 974 76 HOH HOH . H 7 HOH A 75 975 41 HOH HOH . H 7 HOH A 76 976 35 HOH HOH . H 7 HOH A 77 977 187 HOH HOH . H 7 HOH A 78 978 100 HOH HOH . H 7 HOH A 79 979 104 HOH HOH . H 7 HOH A 80 980 18 HOH HOH . H 7 HOH A 81 981 81 HOH HOH . H 7 HOH A 82 982 19 HOH HOH . H 7 HOH A 83 983 107 HOH HOH . H 7 HOH A 84 984 17 HOH HOH . H 7 HOH A 85 985 202 HOH HOH . H 7 HOH A 86 986 152 HOH HOH . H 7 HOH A 87 987 156 HOH HOH . H 7 HOH A 88 988 55 HOH HOH . H 7 HOH A 89 989 61 HOH HOH . H 7 HOH A 90 990 137 HOH HOH . H 7 HOH A 91 991 56 HOH HOH . H 7 HOH A 92 992 92 HOH HOH . H 7 HOH A 93 993 77 HOH HOH . H 7 HOH A 94 994 98 HOH HOH . H 7 HOH A 95 995 108 HOH HOH . H 7 HOH A 96 996 60 HOH HOH . H 7 HOH A 97 997 31 HOH HOH . H 7 HOH A 98 998 93 HOH HOH . H 7 HOH A 99 999 23 HOH HOH . H 7 HOH A 100 1000 36 HOH HOH . H 7 HOH A 101 1001 199 HOH HOH . H 7 HOH A 102 1002 158 HOH HOH . H 7 HOH A 103 1003 69 HOH HOH . H 7 HOH A 104 1004 99 HOH HOH . H 7 HOH A 105 1005 149 HOH HOH . H 7 HOH A 106 1006 80 HOH HOH . H 7 HOH A 107 1007 96 HOH HOH . H 7 HOH A 108 1008 37 HOH HOH . H 7 HOH A 109 1009 75 HOH HOH . H 7 HOH A 110 1010 22 HOH HOH . H 7 HOH A 111 1011 106 HOH HOH . H 7 HOH A 112 1012 65 HOH HOH . H 7 HOH A 113 1013 50 HOH HOH . H 7 HOH A 114 1014 82 HOH HOH . H 7 HOH A 115 1015 62 HOH HOH . H 7 HOH A 116 1016 189 HOH HOH . H 7 HOH A 117 1017 71 HOH HOH . H 7 HOH A 118 1018 73 HOH HOH . H 7 HOH A 119 1019 86 HOH HOH . H 7 HOH A 120 1020 163 HOH HOH . H 7 HOH A 121 1021 33 HOH HOH . H 7 HOH A 122 1022 49 HOH HOH . H 7 HOH A 123 1023 121 HOH HOH . H 7 HOH A 124 1024 135 HOH HOH . H 7 HOH A 125 1025 7 HOH HOH . H 7 HOH A 126 1026 42 HOH HOH . H 7 HOH A 127 1027 129 HOH HOH . H 7 HOH A 128 1028 111 HOH HOH . H 7 HOH A 129 1029 114 HOH HOH . H 7 HOH A 130 1030 25 HOH HOH . H 7 HOH A 131 1031 116 HOH HOH . H 7 HOH A 132 1032 68 HOH HOH . H 7 HOH A 133 1033 125 HOH HOH . H 7 HOH A 134 1034 123 HOH HOH . H 7 HOH A 135 1035 143 HOH HOH . H 7 HOH A 136 1036 205 HOH HOH . H 7 HOH A 137 1037 178 HOH HOH . H 7 HOH A 138 1038 154 HOH HOH . H 7 HOH A 139 1039 134 HOH HOH . H 7 HOH A 140 1040 105 HOH HOH . H 7 HOH A 141 1041 47 HOH HOH . H 7 HOH A 142 1042 169 HOH HOH . H 7 HOH A 143 1043 146 HOH HOH . H 7 HOH A 144 1044 79 HOH HOH . H 7 HOH A 145 1045 26 HOH HOH . H 7 HOH A 146 1046 64 HOH HOH . H 7 HOH A 147 1047 113 HOH HOH . H 7 HOH A 148 1048 38 HOH HOH . H 7 HOH A 149 1049 115 HOH HOH . H 7 HOH A 150 1050 15 HOH HOH . H 7 HOH A 151 1051 95 HOH HOH . H 7 HOH A 152 1052 139 HOH HOH . H 7 HOH A 153 1053 160 HOH HOH . H 7 HOH A 154 1054 103 HOH HOH . H 7 HOH A 155 1055 192 HOH HOH . H 7 HOH A 156 1056 110 HOH HOH . H 7 HOH A 157 1057 66 HOH HOH . H 7 HOH A 158 1058 102 HOH HOH . H 7 HOH A 159 1059 182 HOH HOH . H 7 HOH A 160 1060 128 HOH HOH . H 7 HOH A 161 1061 144 HOH HOH . H 7 HOH A 162 1062 171 HOH HOH . H 7 HOH A 163 1063 168 HOH HOH . H 7 HOH A 164 1064 180 HOH HOH . H 7 HOH A 165 1065 155 HOH HOH . H 7 HOH A 166 1066 203 HOH HOH . H 7 HOH A 167 1067 175 HOH HOH . H 7 HOH A 168 1068 97 HOH HOH . H 7 HOH A 169 1069 90 HOH HOH . H 7 HOH A 170 1070 174 HOH HOH . H 7 HOH A 171 1071 109 HOH HOH . H 7 HOH A 172 1072 130 HOH HOH . H 7 HOH A 173 1073 85 HOH HOH . H 7 HOH A 174 1074 51 HOH HOH . H 7 HOH A 175 1075 161 HOH HOH . H 7 HOH A 176 1076 153 HOH HOH . H 7 HOH A 177 1077 188 HOH HOH . H 7 HOH A 178 1078 193 HOH HOH . H 7 HOH A 179 1079 172 HOH HOH . H 7 HOH A 180 1080 181 HOH HOH . H 7 HOH A 181 1081 124 HOH HOH . H 7 HOH A 182 1082 94 HOH HOH . H 7 HOH A 183 1083 118 HOH HOH . H 7 HOH A 184 1084 195 HOH HOH . H 7 HOH A 185 1085 157 HOH HOH . H 7 HOH A 186 1086 185 HOH HOH . H 7 HOH A 187 1087 166 HOH HOH . H 7 HOH A 188 1088 120 HOH HOH . H 7 HOH A 189 1089 196 HOH HOH . H 7 HOH A 190 1090 136 HOH HOH . H 7 HOH A 191 1091 119 HOH HOH . H 7 HOH A 192 1092 101 HOH HOH . H 7 HOH A 193 1093 147 HOH HOH . H 7 HOH A 194 1094 145 HOH HOH . H 7 HOH A 195 1095 190 HOH HOH . H 7 HOH A 196 1096 177 HOH HOH . H 7 HOH A 197 1097 126 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 GOL . . . F 5 8.632 23.705 -39.383 1 31.46 ? C1 GOL 805 A 1 HETATM 2 O O1 GOL . . . F 5 7.312 23.997 -38.963 1 32.8 ? O1 GOL 805 A 1 HETATM 3 C C2 GOL . . . F 5 9.619 24.123 -38.301 1 29.96 ? C2 GOL 805 A 1 HETATM 4 O O2 GOL . . . F 5 9.443 23.294 -37.179 1 31.86 ? O2 GOL 805 A 1 HETATM 5 C C3 GOL . . . F 5 11.042 23.919 -38.814 1 25.46 ? C3 GOL 805 A 1 HETATM 6 O O3 GOL . . . F 5 11.951 24.581 -37.948 1 25.4 ? O3 GOL 805 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #