data_6QA6 # _model_server_result.job_id dAd1q5UrzVRwVJef8b_wOQ _model_server_result.datetime_utc '2024-11-15 06:39:12' _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 6qa6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1103}' # _entry.id 6QA6 # _exptl.entry_id 6QA6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 358.345 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-2-yl-8,9,10-tris(oxidanyl)-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one _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 6QA6 _cell.length_a 128.161 _cell.length_b 128.161 _cell.length_c 115.794 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QA6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 1,2 # 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' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 115.794 # 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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 681 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 680 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 1104 _struct_conn.ptnr2_symmetry 1_555 _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 1.411 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C18 H18 N2 O6' _chem_comp.formula_weight 358.345 _chem_comp.id HT8 _chem_comp.mon_nstd_flag . _chem_comp.name (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-2-yl-8,9,10-tris(oxidanyl)-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6QA6 _atom_sites.fract_transf_matrix[1][1] 0.007803 _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] 0.007803 _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] 0.008636 _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 DMS A 1 1101 1101 DMS DMS . C 3 HT8 A 1 1102 901 HT8 30 . D 3 HT8 A 1 1103 902 HT8 30 . E 4 PLP A 1 1104 920 PLP PLP . F 5 HOH A 1 1201 350 HOH HOH . F 5 HOH A 2 1202 331 HOH HOH . F 5 HOH A 3 1203 235 HOH HOH . F 5 HOH A 4 1204 229 HOH HOH . F 5 HOH A 5 1205 209 HOH HOH . F 5 HOH A 6 1206 205 HOH HOH . F 5 HOH A 7 1207 153 HOH HOH . F 5 HOH A 8 1208 19 HOH HOH . F 5 HOH A 9 1209 158 HOH HOH . F 5 HOH A 10 1210 96 HOH HOH . F 5 HOH A 11 1211 87 HOH HOH . F 5 HOH A 12 1212 342 HOH HOH . F 5 HOH A 13 1213 258 HOH HOH . F 5 HOH A 14 1214 46 HOH HOH . F 5 HOH A 15 1215 35 HOH HOH . F 5 HOH A 16 1216 137 HOH HOH . F 5 HOH A 17 1217 13 HOH HOH . F 5 HOH A 18 1218 85 HOH HOH . F 5 HOH A 19 1219 173 HOH HOH . F 5 HOH A 20 1220 4 HOH HOH . F 5 HOH A 21 1221 110 HOH HOH . F 5 HOH A 22 1222 271 HOH HOH . F 5 HOH A 23 1223 130 HOH HOH . F 5 HOH A 24 1224 206 HOH HOH . F 5 HOH A 25 1225 80 HOH HOH . F 5 HOH A 26 1226 140 HOH HOH . F 5 HOH A 27 1227 346 HOH HOH . F 5 HOH A 28 1228 336 HOH HOH . F 5 HOH A 29 1229 94 HOH HOH . F 5 HOH A 30 1230 122 HOH HOH . F 5 HOH A 31 1231 65 HOH HOH . F 5 HOH A 32 1232 119 HOH HOH . F 5 HOH A 33 1233 132 HOH HOH . F 5 HOH A 34 1234 11 HOH HOH . F 5 HOH A 35 1235 233 HOH HOH . F 5 HOH A 36 1236 168 HOH HOH . F 5 HOH A 37 1237 311 HOH HOH . F 5 HOH A 38 1238 340 HOH HOH . F 5 HOH A 39 1239 90 HOH HOH . F 5 HOH A 40 1240 59 HOH HOH . F 5 HOH A 41 1241 216 HOH HOH . F 5 HOH A 42 1242 208 HOH HOH . F 5 HOH A 43 1243 214 HOH HOH . F 5 HOH A 44 1244 37 HOH HOH . F 5 HOH A 45 1245 67 HOH HOH . F 5 HOH A 46 1246 16 HOH HOH . F 5 HOH A 47 1247 188 HOH HOH . F 5 HOH A 48 1248 79 HOH HOH . F 5 HOH A 49 1249 166 HOH HOH . F 5 HOH A 50 1250 82 HOH HOH . F 5 HOH A 51 1251 129 HOH HOH . F 5 HOH A 52 1252 200 HOH HOH . F 5 HOH A 53 1253 133 HOH HOH . F 5 HOH A 54 1254 75 HOH HOH . F 5 HOH A 55 1255 148 HOH HOH . F 5 HOH A 56 1256 164 HOH HOH . F 5 HOH A 57 1257 21 HOH HOH . F 5 HOH A 58 1258 360 HOH HOH . F 5 HOH A 59 1259 81 HOH HOH . F 5 HOH A 60 1260 262 HOH HOH . F 5 HOH A 61 1261 84 HOH HOH . F 5 HOH A 62 1262 120 HOH HOH . F 5 HOH A 63 1263 134 HOH HOH . F 5 HOH A 64 1264 92 HOH HOH . F 5 HOH A 65 1265 45 HOH HOH . F 5 HOH A 66 1266 283 HOH HOH . F 5 HOH A 67 1267 139 HOH HOH . F 5 HOH A 68 1268 17 HOH HOH . F 5 HOH A 69 1269 107 HOH HOH . F 5 HOH A 70 1270 50 HOH HOH . F 5 HOH A 71 1271 330 HOH HOH . F 5 HOH A 72 1272 159 HOH HOH . F 5 HOH A 73 1273 22 HOH HOH . F 5 HOH A 74 1274 143 HOH HOH . F 5 HOH A 75 1275 68 HOH HOH . F 5 HOH A 76 1276 225 HOH HOH . F 5 HOH A 77 1277 165 HOH HOH . F 5 HOH A 78 1278 8 HOH HOH . F 5 HOH A 79 1279 53 HOH HOH . F 5 HOH A 80 1280 31 HOH HOH . F 5 HOH A 81 1281 332 HOH HOH . F 5 HOH A 82 1282 280 HOH HOH . F 5 HOH A 83 1283 98 HOH HOH . F 5 HOH A 84 1284 347 HOH HOH . F 5 HOH A 85 1285 34 HOH HOH . F 5 HOH A 86 1286 142 HOH HOH . F 5 HOH A 87 1287 117 HOH HOH . F 5 HOH A 88 1288 30 HOH HOH . F 5 HOH A 89 1289 204 HOH HOH . F 5 HOH A 90 1290 335 HOH HOH . F 5 HOH A 91 1291 240 HOH HOH . F 5 HOH A 92 1292 89 HOH HOH . F 5 HOH A 93 1293 141 HOH HOH . F 5 HOH A 94 1294 38 HOH HOH . F 5 HOH A 95 1295 212 HOH HOH . F 5 HOH A 96 1296 226 HOH HOH . F 5 HOH A 97 1297 58 HOH HOH . F 5 HOH A 98 1298 322 HOH HOH . F 5 HOH A 99 1299 56 HOH HOH . F 5 HOH A 100 1300 7 HOH HOH . F 5 HOH A 101 1301 33 HOH HOH . F 5 HOH A 102 1302 9 HOH HOH . F 5 HOH A 103 1303 343 HOH HOH . F 5 HOH A 104 1304 48 HOH HOH . F 5 HOH A 105 1305 147 HOH HOH . F 5 HOH A 106 1306 327 HOH HOH . F 5 HOH A 107 1307 10 HOH HOH . F 5 HOH A 108 1308 135 HOH HOH . F 5 HOH A 109 1309 41 HOH HOH . F 5 HOH A 110 1310 118 HOH HOH . F 5 HOH A 111 1311 108 HOH HOH . F 5 HOH A 112 1312 3 HOH HOH . F 5 HOH A 113 1313 218 HOH HOH . F 5 HOH A 114 1314 64 HOH HOH . F 5 HOH A 115 1315 95 HOH HOH . F 5 HOH A 116 1316 55 HOH HOH . F 5 HOH A 117 1317 160 HOH HOH . F 5 HOH A 118 1318 29 HOH HOH . F 5 HOH A 119 1319 83 HOH HOH . F 5 HOH A 120 1320 178 HOH HOH . F 5 HOH A 121 1321 97 HOH HOH . F 5 HOH A 122 1322 196 HOH HOH . F 5 HOH A 123 1323 24 HOH HOH . F 5 HOH A 124 1324 52 HOH HOH . F 5 HOH A 125 1325 359 HOH HOH . F 5 HOH A 126 1326 78 HOH HOH . F 5 HOH A 127 1327 152 HOH HOH . F 5 HOH A 128 1328 74 HOH HOH . F 5 HOH A 129 1329 248 HOH HOH . F 5 HOH A 130 1330 109 HOH HOH . F 5 HOH A 131 1331 263 HOH HOH . F 5 HOH A 132 1332 18 HOH HOH . F 5 HOH A 133 1333 219 HOH HOH . F 5 HOH A 134 1334 328 HOH HOH . F 5 HOH A 135 1335 154 HOH HOH . F 5 HOH A 136 1336 203 HOH HOH . F 5 HOH A 137 1337 202 HOH HOH . F 5 HOH A 138 1338 73 HOH HOH . F 5 HOH A 139 1339 156 HOH HOH . F 5 HOH A 140 1340 91 HOH HOH . F 5 HOH A 141 1341 123 HOH HOH . F 5 HOH A 142 1342 163 HOH HOH . F 5 HOH A 143 1343 210 HOH HOH . F 5 HOH A 144 1344 146 HOH HOH . F 5 HOH A 145 1345 321 HOH HOH . F 5 HOH A 146 1346 23 HOH HOH . F 5 HOH A 147 1347 355 HOH HOH . F 5 HOH A 148 1348 5 HOH HOH . F 5 HOH A 149 1349 51 HOH HOH . F 5 HOH A 150 1350 54 HOH HOH . F 5 HOH A 151 1351 334 HOH HOH . F 5 HOH A 152 1352 126 HOH HOH . F 5 HOH A 153 1353 187 HOH HOH . F 5 HOH A 154 1354 181 HOH HOH . F 5 HOH A 155 1355 176 HOH HOH . F 5 HOH A 156 1356 194 HOH HOH . F 5 HOH A 157 1357 111 HOH HOH . F 5 HOH A 158 1358 49 HOH HOH . F 5 HOH A 159 1359 223 HOH HOH . F 5 HOH A 160 1360 93 HOH HOH . F 5 HOH A 161 1361 162 HOH HOH . F 5 HOH A 162 1362 116 HOH HOH . F 5 HOH A 163 1363 255 HOH HOH . F 5 HOH A 164 1364 167 HOH HOH . F 5 HOH A 165 1365 57 HOH HOH . F 5 HOH A 166 1366 329 HOH HOH . F 5 HOH A 167 1367 40 HOH HOH . F 5 HOH A 168 1368 184 HOH HOH . F 5 HOH A 169 1369 86 HOH HOH . F 5 HOH A 170 1370 113 HOH HOH . F 5 HOH A 171 1371 14 HOH HOH . F 5 HOH A 172 1372 15 HOH HOH . F 5 HOH A 173 1373 77 HOH HOH . F 5 HOH A 174 1374 254 HOH HOH . F 5 HOH A 175 1375 191 HOH HOH . F 5 HOH A 176 1376 36 HOH HOH . F 5 HOH A 177 1377 112 HOH HOH . F 5 HOH A 178 1378 207 HOH HOH . F 5 HOH A 179 1379 217 HOH HOH . F 5 HOH A 180 1380 272 HOH HOH . F 5 HOH A 181 1381 131 HOH HOH . F 5 HOH A 182 1382 232 HOH HOH . F 5 HOH A 183 1383 352 HOH HOH . F 5 HOH A 184 1384 220 HOH HOH . F 5 HOH A 185 1385 193 HOH HOH . F 5 HOH A 186 1386 253 HOH HOH . F 5 HOH A 187 1387 39 HOH HOH . F 5 HOH A 188 1388 354 HOH HOH . F 5 HOH A 189 1389 269 HOH HOH . F 5 HOH A 190 1390 70 HOH HOH . F 5 HOH A 191 1391 189 HOH HOH . F 5 HOH A 192 1392 190 HOH HOH . F 5 HOH A 193 1393 66 HOH HOH . F 5 HOH A 194 1394 138 HOH HOH . F 5 HOH A 195 1395 252 HOH HOH . F 5 HOH A 196 1396 12 HOH HOH . F 5 HOH A 197 1397 284 HOH HOH . F 5 HOH A 198 1398 351 HOH HOH . F 5 HOH A 199 1399 6 HOH HOH . F 5 HOH A 200 1400 25 HOH HOH . F 5 HOH A 201 1401 199 HOH HOH . F 5 HOH A 202 1402 72 HOH HOH . F 5 HOH A 203 1403 169 HOH HOH . F 5 HOH A 204 1404 44 HOH HOH . F 5 HOH A 205 1405 121 HOH HOH . F 5 HOH A 206 1406 43 HOH HOH . F 5 HOH A 207 1407 20 HOH HOH . F 5 HOH A 208 1408 127 HOH HOH . F 5 HOH A 209 1409 295 HOH HOH . F 5 HOH A 210 1410 151 HOH HOH . F 5 HOH A 211 1411 32 HOH HOH . F 5 HOH A 212 1412 198 HOH HOH . F 5 HOH A 213 1413 171 HOH HOH . F 5 HOH A 214 1414 242 HOH HOH . F 5 HOH A 215 1415 247 HOH HOH . F 5 HOH A 216 1416 333 HOH HOH . F 5 HOH A 217 1417 150 HOH HOH . F 5 HOH A 218 1418 88 HOH HOH . F 5 HOH A 219 1419 124 HOH HOH . F 5 HOH A 220 1420 246 HOH HOH . F 5 HOH A 221 1421 356 HOH HOH . F 5 HOH A 222 1422 186 HOH HOH . F 5 HOH A 223 1423 324 HOH HOH . F 5 HOH A 224 1424 358 HOH HOH . F 5 HOH A 225 1425 265 HOH HOH . F 5 HOH A 226 1426 361 HOH HOH . F 5 HOH A 227 1427 345 HOH HOH . F 5 HOH A 228 1428 357 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 C2' HT8 . . . D 3 16.479 13.376 58.273 1 56.57 ? C2' HT8 1103 A 1 HETATM 2 C C3' HT8 . . . D 3 16.72 14.427 59.35 1 61.01 ? C3' HT8 1103 A 1 HETATM 3 C C4' HT8 . . . D 3 18.003 14.101 60.11 1 75.56 ? C4' HT8 1103 A 1 HETATM 4 C C5' HT8 . . . D 3 19.164 14.033 59.108 1 79.17 ? C5' HT8 1103 A 1 HETATM 5 O O5' HT8 . . . D 3 18.899 13.021 58.114 1 69.82 ? O5' HT8 1103 A 1 HETATM 6 C C1' HT8 . . . D 3 17.711 13.217 57.37 1 58.37 ? C1' HT8 1103 A 1 HETATM 7 N N1 HT8 . . . D 3 17.575 12.081 56.445 1 44.88 ? N1 HT8 1103 A 1 HETATM 8 C C2 HT8 . . . D 3 17.658 12.548 55.232 1 49.35 ? C2 HT8 1103 A 1 HETATM 9 N N3 HT8 . . . D 3 17.874 13.884 55.19 1 47.72 ? N3 HT8 1103 A 1 HETATM 10 C C4 HT8 . . . D 3 17.848 14.385 56.452 1 53.02 ? C4 HT8 1103 A 1 HETATM 11 O O4 HT8 . . . D 3 17.904 15.561 56.756 1 44.3 ? O4 HT8 1103 A 1 HETATM 12 C C5 HT8 . . . D 3 17.504 11.721 54.033 1 49.7 ? C5 HT8 1103 A 1 HETATM 13 C C6 HT8 . . . D 3 16.808 10.488 54.08 1 51.28 ? C6 HT8 1103 A 1 HETATM 14 C C7 HT8 . . . D 3 16.651 9.737 52.954 1 49.59 ? C7 HT8 1103 A 1 HETATM 15 C C8 HT8 . . . D 3 17.182 10.172 51.716 1 52.85 ? C8 HT8 1103 A 1 HETATM 16 C C9 HT8 . . . D 3 17.878 11.409 51.661 1 45.82 ? C9 HT8 1103 A 1 HETATM 17 C C10 HT8 . . . D 3 18.02 12.165 52.846 1 50.52 ? C10 HT8 1103 A 1 HETATM 18 C C11 HT8 . . . D 3 17.04 9.423 50.517 1 48.12 ? C11 HT8 1103 A 1 HETATM 19 C C12 HT8 . . . D 3 17.554 9.884 49.346 1 52.46 ? C12 HT8 1103 A 1 HETATM 20 C C13 HT8 . . . D 3 18.245 11.107 49.3 1 49.21 ? C13 HT8 1103 A 1 HETATM 21 C C14 HT8 . . . D 3 18.404 11.848 50.425 1 40.8 ? C14 HT8 1103 A 1 HETATM 22 O O2' HT8 . . . D 3 15.347 13.721 57.468 1 59.03 ? O2' HT8 1103 A 1 HETATM 23 O O3' HT8 . . . D 3 15.602 14.485 60.239 1 49.06 ? O3' HT8 1103 A 1 HETATM 24 O O4' HT8 . . . D 3 18.232 15.094 61.112 1 62.23 ? O4' HT8 1103 A 1 HETATM 25 C C6' HT8 . . . D 3 20.501 13.657 59.706 1 73.56 ? C6' HT8 1103 A 1 HETATM 26 O O6' HT8 . . . D 3 20.526 12.275 60.061 1 69.61 ? O6' HT8 1103 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 26 #