data_1YE8 # _model_server_result.job_id MIZFTcEWGzZocyatkX5jpQ _model_server_result.datetime_utc '2024-11-29 13:56:44' _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 1ye8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1004}' # _entry.id 1YE8 # _exptl.entry_id 1YE8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 105.23 _cell.angle_gamma 90 _cell.entry_id 1YE8 _cell.length_a 35.87 _cell.length_b 64.24 _cell.length_c 39.62 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YE8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 ? 3 C N N ? 3 D 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 MSE 1 A MSE 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C LYS 110 A LYS 110 1_555 A N MSE 111 A MSE 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C MSE 111 A MSE 111 1_555 A N GLU 112 A GLU 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale4 A C ILE 125 A ILE 125 1_555 A N MSE 126 A MSE 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C MSE 126 A MSE 126 1_555 A N HIS 127 A HIS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A O GLU 8 A GLU 8 1_555 C NA NA . A NA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc2 A NZ LYS 13 A LYS 13 1_555 C NA NA . A NA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc3 A OG1 THR 14 A THR 14 1_555 B MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc4 E O1 PO4 . A PO4 1001 1_555 B MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc5 E O3 PO4 . A PO4 1001 1_555 C NA NA . A NA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc6 E O2 PO4 . A PO4 1001 1_555 D NA NA . A NA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc7 B MG MG . A MG 1002 1_555 F O HOH . A HOH 1028 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc8 B MG MG . A MG 1002 1_555 F O HOH . A HOH 1135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc9 B MG MG . A MG 1002 1_555 F O HOH . A HOH 1227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc10 B MG MG . A MG 1002 1_555 F O HOH . A HOH 1252 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.001 ? metalc ? metalc11 C NA NA . A NA 1003 1_555 F O HOH . A HOH 1247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc12 D NA NA . A NA 1004 1_555 F O HOH . A HOH 1227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc13 D NA NA . A NA 1004 1_555 F O HOH . A HOH 1250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1YE8 _atom_sites.fract_transf_matrix[1][1] 0.027878 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00759 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015567 _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] 0.026158 _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 MG A 1 1002 1002 MG MG . C 3 NA A 1 1003 1003 NA NA . D 3 NA A 1 1004 1004 NA NA . E 4 PO4 A 1 1001 1001 PO4 PO4 . F 5 HOH A 1 1005 1 HOH HOH . F 5 HOH A 2 1006 2 HOH HOH . F 5 HOH A 3 1007 3 HOH HOH . F 5 HOH A 4 1008 4 HOH HOH . F 5 HOH A 5 1009 5 HOH HOH . F 5 HOH A 6 1010 6 HOH HOH . F 5 HOH A 7 1011 7 HOH HOH . F 5 HOH A 8 1012 8 HOH HOH . F 5 HOH A 9 1013 9 HOH HOH . F 5 HOH A 10 1014 10 HOH HOH . F 5 HOH A 11 1015 11 HOH HOH . F 5 HOH A 12 1016 12 HOH HOH . F 5 HOH A 13 1017 13 HOH HOH . F 5 HOH A 14 1018 14 HOH HOH . F 5 HOH A 15 1019 15 HOH HOH . F 5 HOH A 16 1020 16 HOH HOH . F 5 HOH A 17 1021 17 HOH HOH . F 5 HOH A 18 1022 18 HOH HOH . F 5 HOH A 19 1023 19 HOH HOH . F 5 HOH A 20 1024 20 HOH HOH . F 5 HOH A 21 1025 21 HOH HOH . F 5 HOH A 22 1026 22 HOH HOH . F 5 HOH A 23 1027 23 HOH HOH . F 5 HOH A 24 1028 24 HOH HOH . F 5 HOH A 25 1029 25 HOH HOH . F 5 HOH A 26 1030 26 HOH HOH . F 5 HOH A 27 1031 27 HOH HOH . F 5 HOH A 28 1032 28 HOH HOH . F 5 HOH A 29 1033 29 HOH HOH . F 5 HOH A 30 1034 30 HOH HOH . F 5 HOH A 31 1035 31 HOH HOH . F 5 HOH A 32 1036 32 HOH HOH . F 5 HOH A 33 1037 33 HOH HOH . F 5 HOH A 34 1038 34 HOH HOH . F 5 HOH A 35 1039 35 HOH HOH . F 5 HOH A 36 1040 36 HOH HOH . F 5 HOH A 37 1041 37 HOH HOH . F 5 HOH A 38 1042 38 HOH HOH . F 5 HOH A 39 1043 39 HOH HOH . F 5 HOH A 40 1044 40 HOH HOH . F 5 HOH A 41 1045 41 HOH HOH . F 5 HOH A 42 1046 42 HOH HOH . F 5 HOH A 43 1047 43 HOH HOH . F 5 HOH A 44 1048 44 HOH HOH . F 5 HOH A 45 1049 45 HOH HOH . F 5 HOH A 46 1050 46 HOH HOH . F 5 HOH A 47 1051 47 HOH HOH . F 5 HOH A 48 1052 48 HOH HOH . F 5 HOH A 49 1053 49 HOH HOH . F 5 HOH A 50 1054 50 HOH HOH . F 5 HOH A 51 1055 51 HOH HOH . F 5 HOH A 52 1056 52 HOH HOH . F 5 HOH A 53 1057 53 HOH HOH . F 5 HOH A 54 1058 54 HOH HOH . F 5 HOH A 55 1059 55 HOH HOH . F 5 HOH A 56 1060 56 HOH HOH . F 5 HOH A 57 1061 57 HOH HOH . F 5 HOH A 58 1062 58 HOH HOH . F 5 HOH A 59 1063 59 HOH HOH . F 5 HOH A 60 1064 60 HOH HOH . F 5 HOH A 61 1065 61 HOH HOH . F 5 HOH A 62 1066 62 HOH HOH . F 5 HOH A 63 1067 63 HOH HOH . F 5 HOH A 64 1068 64 HOH HOH . F 5 HOH A 65 1069 65 HOH HOH . F 5 HOH A 66 1070 66 HOH HOH . F 5 HOH A 67 1071 67 HOH HOH . F 5 HOH A 68 1072 68 HOH HOH . F 5 HOH A 69 1073 69 HOH HOH . F 5 HOH A 70 1074 70 HOH HOH . F 5 HOH A 71 1075 71 HOH HOH . F 5 HOH A 72 1076 72 HOH HOH . F 5 HOH A 73 1077 73 HOH HOH . F 5 HOH A 74 1078 74 HOH HOH . F 5 HOH A 75 1079 75 HOH HOH . F 5 HOH A 76 1080 76 HOH HOH . F 5 HOH A 77 1081 77 HOH HOH . F 5 HOH A 78 1082 78 HOH HOH . F 5 HOH A 79 1083 79 HOH HOH . F 5 HOH A 80 1084 80 HOH HOH . F 5 HOH A 81 1085 81 HOH HOH . F 5 HOH A 82 1086 82 HOH HOH . F 5 HOH A 83 1087 83 HOH HOH . F 5 HOH A 84 1088 84 HOH HOH . F 5 HOH A 85 1089 85 HOH HOH . F 5 HOH A 86 1090 86 HOH HOH . F 5 HOH A 87 1091 87 HOH HOH . F 5 HOH A 88 1092 88 HOH HOH . F 5 HOH A 89 1093 89 HOH HOH . F 5 HOH A 90 1094 90 HOH HOH . F 5 HOH A 91 1095 91 HOH HOH . F 5 HOH A 92 1096 92 HOH HOH . F 5 HOH A 93 1097 93 HOH HOH . F 5 HOH A 94 1098 94 HOH HOH . F 5 HOH A 95 1099 95 HOH HOH . F 5 HOH A 96 1100 96 HOH HOH . F 5 HOH A 97 1101 97 HOH HOH . F 5 HOH A 98 1102 98 HOH HOH . F 5 HOH A 99 1103 99 HOH HOH . F 5 HOH A 100 1104 100 HOH HOH . F 5 HOH A 101 1105 101 HOH HOH . F 5 HOH A 102 1106 102 HOH HOH . F 5 HOH A 103 1107 103 HOH HOH . F 5 HOH A 104 1108 104 HOH HOH . F 5 HOH A 105 1109 105 HOH HOH . F 5 HOH A 106 1110 106 HOH HOH . F 5 HOH A 107 1111 107 HOH HOH . F 5 HOH A 108 1112 108 HOH HOH . F 5 HOH A 109 1113 109 HOH HOH . F 5 HOH A 110 1114 110 HOH HOH . F 5 HOH A 111 1115 111 HOH HOH . F 5 HOH A 112 1116 112 HOH HOH . F 5 HOH A 113 1117 113 HOH HOH . F 5 HOH A 114 1118 114 HOH HOH . F 5 HOH A 115 1119 115 HOH HOH . F 5 HOH A 116 1120 116 HOH HOH . F 5 HOH A 117 1121 117 HOH HOH . F 5 HOH A 118 1122 118 HOH HOH . F 5 HOH A 119 1123 119 HOH HOH . F 5 HOH A 120 1124 120 HOH HOH . F 5 HOH A 121 1125 121 HOH HOH . F 5 HOH A 122 1126 122 HOH HOH . F 5 HOH A 123 1127 123 HOH HOH . F 5 HOH A 124 1128 124 HOH HOH . F 5 HOH A 125 1129 125 HOH HOH . F 5 HOH A 126 1130 126 HOH HOH . F 5 HOH A 127 1131 127 HOH HOH . F 5 HOH A 128 1132 128 HOH HOH . F 5 HOH A 129 1133 129 HOH HOH . F 5 HOH A 130 1134 130 HOH HOH . F 5 HOH A 131 1135 131 HOH HOH . F 5 HOH A 132 1136 132 HOH HOH . F 5 HOH A 133 1137 133 HOH HOH . F 5 HOH A 134 1138 134 HOH HOH . F 5 HOH A 135 1139 135 HOH HOH . F 5 HOH A 136 1140 136 HOH HOH . F 5 HOH A 137 1141 137 HOH HOH . F 5 HOH A 138 1142 138 HOH HOH . F 5 HOH A 139 1143 139 HOH HOH . F 5 HOH A 140 1144 140 HOH HOH . F 5 HOH A 141 1145 141 HOH HOH . F 5 HOH A 142 1146 142 HOH HOH . F 5 HOH A 143 1147 143 HOH HOH . F 5 HOH A 144 1148 144 HOH HOH . F 5 HOH A 145 1149 145 HOH HOH . F 5 HOH A 146 1150 146 HOH HOH . F 5 HOH A 147 1151 147 HOH HOH . F 5 HOH A 148 1152 148 HOH HOH . F 5 HOH A 149 1153 149 HOH HOH . F 5 HOH A 150 1154 150 HOH HOH . F 5 HOH A 151 1155 151 HOH HOH . F 5 HOH A 152 1156 152 HOH HOH . F 5 HOH A 153 1157 153 HOH HOH . F 5 HOH A 154 1158 154 HOH HOH . F 5 HOH A 155 1159 155 HOH HOH . F 5 HOH A 156 1160 156 HOH HOH . F 5 HOH A 157 1161 157 HOH HOH . F 5 HOH A 158 1162 158 HOH HOH . F 5 HOH A 159 1163 160 HOH HOH . F 5 HOH A 160 1164 161 HOH HOH . F 5 HOH A 161 1165 162 HOH HOH . F 5 HOH A 162 1166 163 HOH HOH . F 5 HOH A 163 1167 164 HOH HOH . F 5 HOH A 164 1168 165 HOH HOH . F 5 HOH A 165 1169 166 HOH HOH . F 5 HOH A 166 1170 167 HOH HOH . F 5 HOH A 167 1171 168 HOH HOH . F 5 HOH A 168 1172 169 HOH HOH . F 5 HOH A 169 1173 170 HOH HOH . F 5 HOH A 170 1174 171 HOH HOH . F 5 HOH A 171 1175 172 HOH HOH . F 5 HOH A 172 1176 173 HOH HOH . F 5 HOH A 173 1177 174 HOH HOH . F 5 HOH A 174 1178 175 HOH HOH . F 5 HOH A 175 1179 176 HOH HOH . F 5 HOH A 176 1180 177 HOH HOH . F 5 HOH A 177 1181 178 HOH HOH . F 5 HOH A 178 1182 179 HOH HOH . F 5 HOH A 179 1183 180 HOH HOH . F 5 HOH A 180 1184 181 HOH HOH . F 5 HOH A 181 1185 182 HOH HOH . F 5 HOH A 182 1186 183 HOH HOH . F 5 HOH A 183 1187 184 HOH HOH . F 5 HOH A 184 1188 185 HOH HOH . F 5 HOH A 185 1189 186 HOH HOH . F 5 HOH A 186 1190 187 HOH HOH . F 5 HOH A 187 1191 188 HOH HOH . F 5 HOH A 188 1192 189 HOH HOH . F 5 HOH A 189 1193 190 HOH HOH . F 5 HOH A 190 1194 191 HOH HOH . F 5 HOH A 191 1195 192 HOH HOH . F 5 HOH A 192 1196 193 HOH HOH . F 5 HOH A 193 1197 194 HOH HOH . F 5 HOH A 194 1198 195 HOH HOH . F 5 HOH A 195 1199 196 HOH HOH . F 5 HOH A 196 1200 197 HOH HOH . F 5 HOH A 197 1201 198 HOH HOH . F 5 HOH A 198 1202 199 HOH HOH . F 5 HOH A 199 1203 200 HOH HOH . F 5 HOH A 200 1204 201 HOH HOH . F 5 HOH A 201 1205 202 HOH HOH . F 5 HOH A 202 1206 203 HOH HOH . F 5 HOH A 203 1207 204 HOH HOH . F 5 HOH A 204 1208 205 HOH HOH . F 5 HOH A 205 1209 206 HOH HOH . F 5 HOH A 206 1210 207 HOH HOH . F 5 HOH A 207 1211 208 HOH HOH . F 5 HOH A 208 1212 209 HOH HOH . F 5 HOH A 209 1213 210 HOH HOH . F 5 HOH A 210 1214 211 HOH HOH . F 5 HOH A 211 1215 212 HOH HOH . F 5 HOH A 212 1216 213 HOH HOH . F 5 HOH A 213 1217 214 HOH HOH . F 5 HOH A 214 1218 215 HOH HOH . F 5 HOH A 215 1219 216 HOH HOH . F 5 HOH A 216 1220 217 HOH HOH . F 5 HOH A 217 1221 218 HOH HOH . F 5 HOH A 218 1222 219 HOH HOH . F 5 HOH A 219 1223 220 HOH HOH . F 5 HOH A 220 1224 221 HOH HOH . F 5 HOH A 221 1225 222 HOH HOH . F 5 HOH A 222 1226 223 HOH HOH . F 5 HOH A 223 1227 224 HOH HOH . F 5 HOH A 224 1228 225 HOH HOH . F 5 HOH A 225 1229 226 HOH HOH . F 5 HOH A 226 1230 227 HOH HOH . F 5 HOH A 227 1231 228 HOH HOH . F 5 HOH A 228 1232 229 HOH HOH . F 5 HOH A 229 1233 230 HOH HOH . F 5 HOH A 230 1234 231 HOH HOH . F 5 HOH A 231 1235 232 HOH HOH . F 5 HOH A 232 1236 233 HOH HOH . F 5 HOH A 233 1237 234 HOH HOH . F 5 HOH A 234 1238 235 HOH HOH . F 5 HOH A 235 1239 236 HOH HOH . F 5 HOH A 236 1240 237 HOH HOH . F 5 HOH A 237 1241 238 HOH HOH . F 5 HOH A 238 1242 239 HOH HOH . F 5 HOH A 239 1243 240 HOH HOH . F 5 HOH A 240 1244 241 HOH HOH . F 5 HOH A 241 1245 242 HOH HOH . F 5 HOH A 242 1246 243 HOH HOH . F 5 HOH A 243 1247 244 HOH HOH . F 5 HOH A 244 1248 245 HOH HOH . F 5 HOH A 245 1249 246 HOH HOH . F 5 HOH A 246 1250 247 HOH HOH . F 5 HOH A 247 1251 248 HOH HOH . F 5 HOH A 248 1252 249 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x 37.696 _atom_site.Cartn_y 32.464 _atom_site.Cartn_z 34.068 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 29.54 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1004 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #