data_2ZDA # _model_server_result.job_id ouNOIO2PmqkxBy4dBjB-HQ _model_server_result.datetime_utc '2024-10-12 15:27:47' _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 2zda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1100}' # _entry.id 2ZDA # _exptl.entry_id 2ZDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _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 100.5 _cell.angle_gamma 90 _cell.entry_id 2ZDA _cell.length_a 70.3 _cell.length_b 71.5 _cell.length_c 72.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J _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 ? 4 D N N ? 4 E 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 disulf ? disulf1 A SG CYS 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? covale ? covale1 C C GLU 9 I GLU 62 1_555 C N TYS 10 I TYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 C C TYS 10 I TYS 63 1_555 C N LEU 11 I LEU 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _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 2ZDA _atom_sites.fract_transf_matrix[1][1] 0.014228 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00264 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013979 _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] 0.014047 _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 D 4 NA H 1 1100 1100 NA NA . E 4 NA H 1 1101 1101 NA NA . F 5 PO4 H 1 1102 1102 PO4 PO4 . G 6 32U H 1 1000 1000 32U 32U . H 7 HOH L 1 1201 1201 HOH HOH . H 7 HOH L 2 1207 1207 HOH HOH . H 7 HOH L 3 1210 1210 HOH HOH . H 7 HOH L 4 1222 1222 HOH HOH . H 7 HOH L 5 1235 1235 HOH HOH . H 7 HOH L 6 1259 1259 HOH HOH . H 7 HOH L 7 1260 1260 HOH HOH . H 7 HOH L 8 1275 1275 HOH HOH . H 7 HOH L 9 1277 1277 HOH HOH . H 7 HOH L 10 1281 1281 HOH HOH . H 7 HOH L 11 1287 1287 HOH HOH . H 7 HOH L 12 1291 1291 HOH HOH . H 7 HOH L 13 1295 1295 HOH HOH . H 7 HOH L 14 1299 1299 HOH HOH . H 7 HOH L 15 1305 1305 HOH HOH . H 7 HOH L 16 1336 1336 HOH HOH . H 7 HOH L 17 1338 1338 HOH HOH . H 7 HOH L 18 1339 1339 HOH HOH . H 7 HOH L 19 1341 1341 HOH HOH . H 7 HOH L 20 1349 1349 HOH HOH . H 7 HOH L 21 1368 1368 HOH HOH . H 7 HOH L 22 1376 1376 HOH HOH . H 7 HOH L 23 1389 1389 HOH HOH . H 7 HOH L 24 1392 1392 HOH HOH . H 7 HOH L 25 1415 1415 HOH HOH . H 7 HOH L 26 1423 1423 HOH HOH . H 7 HOH L 27 1427 1427 HOH HOH . H 7 HOH L 28 1429 1429 HOH HOH . H 7 HOH L 29 1441 1441 HOH HOH . H 7 HOH L 30 1453 1453 HOH HOH . H 7 HOH L 31 1457 1457 HOH HOH . H 7 HOH L 32 1462 1462 HOH HOH . H 7 HOH L 33 1464 1464 HOH HOH . I 7 HOH H 1 1202 1202 HOH HOH . I 7 HOH H 2 1203 1203 HOH HOH . I 7 HOH H 3 1204 1204 HOH HOH . I 7 HOH H 4 1205 1205 HOH HOH . I 7 HOH H 5 1206 1206 HOH HOH . I 7 HOH H 6 1208 1208 HOH HOH . I 7 HOH H 7 1209 1209 HOH HOH . I 7 HOH H 8 1211 1211 HOH HOH . I 7 HOH H 9 1212 1212 HOH HOH . I 7 HOH H 10 1213 1213 HOH HOH . I 7 HOH H 11 1214 1214 HOH HOH . I 7 HOH H 12 1215 1215 HOH HOH . I 7 HOH H 13 1216 1216 HOH HOH . I 7 HOH H 14 1217 1217 HOH HOH . I 7 HOH H 15 1218 1218 HOH HOH . I 7 HOH H 16 1219 1219 HOH HOH . I 7 HOH H 17 1220 1220 HOH HOH . I 7 HOH H 18 1221 1221 HOH HOH . I 7 HOH H 19 1223 1223 HOH HOH . I 7 HOH H 20 1224 1224 HOH HOH . I 7 HOH H 21 1225 1225 HOH HOH . I 7 HOH H 22 1226 1226 HOH HOH . I 7 HOH H 23 1227 1227 HOH HOH . I 7 HOH H 24 1228 1228 HOH HOH . I 7 HOH H 25 1229 1229 HOH HOH . I 7 HOH H 26 1230 1230 HOH HOH . I 7 HOH H 27 1231 1231 HOH HOH . I 7 HOH H 28 1232 1232 HOH HOH . I 7 HOH H 29 1233 1233 HOH HOH . I 7 HOH H 30 1234 1234 HOH HOH . I 7 HOH H 31 1236 1236 HOH HOH . I 7 HOH H 32 1237 1237 HOH HOH . I 7 HOH H 33 1238 1238 HOH HOH . I 7 HOH H 34 1239 1239 HOH HOH . I 7 HOH H 35 1240 1240 HOH HOH . I 7 HOH H 36 1241 1241 HOH HOH . I 7 HOH H 37 1242 1242 HOH HOH . I 7 HOH H 38 1243 1243 HOH HOH . I 7 HOH H 39 1244 1244 HOH HOH . I 7 HOH H 40 1245 1245 HOH HOH . I 7 HOH H 41 1246 1246 HOH HOH . I 7 HOH H 42 1247 1247 HOH HOH . I 7 HOH H 43 1248 1248 HOH HOH . I 7 HOH H 44 1249 1249 HOH HOH . I 7 HOH H 45 1250 1250 HOH HOH . I 7 HOH H 46 1251 1251 HOH HOH . I 7 HOH H 47 1252 1252 HOH HOH . I 7 HOH H 48 1253 1253 HOH HOH . I 7 HOH H 49 1254 1254 HOH HOH . I 7 HOH H 50 1255 1255 HOH HOH . I 7 HOH H 51 1256 1256 HOH HOH . I 7 HOH H 52 1257 1257 HOH HOH . I 7 HOH H 53 1258 1258 HOH HOH . I 7 HOH H 54 1261 1261 HOH HOH . I 7 HOH H 55 1262 1262 HOH HOH . I 7 HOH H 56 1263 1263 HOH HOH . I 7 HOH H 57 1264 1264 HOH HOH . I 7 HOH H 58 1265 1265 HOH HOH . I 7 HOH H 59 1266 1266 HOH HOH . I 7 HOH H 60 1267 1267 HOH HOH . I 7 HOH H 61 1268 1268 HOH HOH . I 7 HOH H 62 1269 1269 HOH HOH . I 7 HOH H 63 1270 1270 HOH HOH . I 7 HOH H 64 1271 1271 HOH HOH . I 7 HOH H 65 1272 1272 HOH HOH . I 7 HOH H 66 1273 1273 HOH HOH . I 7 HOH H 67 1274 1274 HOH HOH . I 7 HOH H 68 1276 1276 HOH HOH . I 7 HOH H 69 1278 1278 HOH HOH . I 7 HOH H 70 1279 1279 HOH HOH . I 7 HOH H 71 1280 1280 HOH HOH . I 7 HOH H 72 1282 1282 HOH HOH . I 7 HOH H 73 1283 1283 HOH HOH . I 7 HOH H 74 1284 1284 HOH HOH . I 7 HOH H 75 1285 1285 HOH HOH . I 7 HOH H 76 1286 1286 HOH HOH . I 7 HOH H 77 1288 1288 HOH HOH . I 7 HOH H 78 1289 1289 HOH HOH . I 7 HOH H 79 1290 1290 HOH HOH . I 7 HOH H 80 1292 1292 HOH HOH . I 7 HOH H 81 1293 1293 HOH HOH . I 7 HOH H 82 1294 1294 HOH HOH . I 7 HOH H 83 1296 1296 HOH HOH . I 7 HOH H 84 1297 1297 HOH HOH . I 7 HOH H 85 1298 1298 HOH HOH . I 7 HOH H 86 1300 1300 HOH HOH . I 7 HOH H 87 1301 1301 HOH HOH . I 7 HOH H 88 1302 1302 HOH HOH . I 7 HOH H 89 1303 1303 HOH HOH . I 7 HOH H 90 1304 1304 HOH HOH . I 7 HOH H 91 1306 1306 HOH HOH . I 7 HOH H 92 1307 1307 HOH HOH . I 7 HOH H 93 1308 1308 HOH HOH . I 7 HOH H 94 1309 1309 HOH HOH . I 7 HOH H 95 1310 1310 HOH HOH . I 7 HOH H 96 1311 1311 HOH HOH . I 7 HOH H 97 1312 1312 HOH HOH . I 7 HOH H 98 1313 1313 HOH HOH . I 7 HOH H 99 1314 1314 HOH HOH . I 7 HOH H 100 1315 1315 HOH HOH . I 7 HOH H 101 1316 1316 HOH HOH . I 7 HOH H 102 1317 1317 HOH HOH . I 7 HOH H 103 1318 1318 HOH HOH . I 7 HOH H 104 1319 1319 HOH HOH . I 7 HOH H 105 1320 1320 HOH HOH . I 7 HOH H 106 1321 1321 HOH HOH . I 7 HOH H 107 1322 1322 HOH HOH . I 7 HOH H 108 1323 1323 HOH HOH . I 7 HOH H 109 1324 1324 HOH HOH . I 7 HOH H 110 1325 1325 HOH HOH . I 7 HOH H 111 1326 1326 HOH HOH . I 7 HOH H 112 1327 1327 HOH HOH . I 7 HOH H 113 1328 1328 HOH HOH . I 7 HOH H 114 1329 1329 HOH HOH . I 7 HOH H 115 1330 1330 HOH HOH . I 7 HOH H 116 1331 1331 HOH HOH . I 7 HOH H 117 1332 1332 HOH HOH . I 7 HOH H 118 1333 1333 HOH HOH . I 7 HOH H 119 1335 1335 HOH HOH . I 7 HOH H 120 1337 1337 HOH HOH . I 7 HOH H 121 1340 1340 HOH HOH . I 7 HOH H 122 1342 1342 HOH HOH . I 7 HOH H 123 1343 1343 HOH HOH . I 7 HOH H 124 1344 1344 HOH HOH . I 7 HOH H 125 1345 1345 HOH HOH . I 7 HOH H 126 1346 1346 HOH HOH . I 7 HOH H 127 1347 1347 HOH HOH . I 7 HOH H 128 1348 1348 HOH HOH . I 7 HOH H 129 1350 1350 HOH HOH . I 7 HOH H 130 1351 1351 HOH HOH . I 7 HOH H 131 1352 1352 HOH HOH . I 7 HOH H 132 1353 1353 HOH HOH . I 7 HOH H 133 1354 1354 HOH HOH . I 7 HOH H 134 1355 1355 HOH HOH . I 7 HOH H 135 1357 1357 HOH HOH . I 7 HOH H 136 1358 1358 HOH HOH . I 7 HOH H 137 1359 1359 HOH HOH . I 7 HOH H 138 1360 1360 HOH HOH . I 7 HOH H 139 1361 1361 HOH HOH . I 7 HOH H 140 1362 1362 HOH HOH . I 7 HOH H 141 1363 1363 HOH HOH . I 7 HOH H 142 1364 1364 HOH HOH . I 7 HOH H 143 1365 1365 HOH HOH . I 7 HOH H 144 1366 1366 HOH HOH . I 7 HOH H 145 1367 1367 HOH HOH . I 7 HOH H 146 1369 1369 HOH HOH . I 7 HOH H 147 1370 1370 HOH HOH . I 7 HOH H 148 1371 1371 HOH HOH . I 7 HOH H 149 1372 1372 HOH HOH . I 7 HOH H 150 1373 1373 HOH HOH . I 7 HOH H 151 1374 1374 HOH HOH . I 7 HOH H 152 1375 1375 HOH HOH . I 7 HOH H 153 1377 1377 HOH HOH . I 7 HOH H 154 1378 1378 HOH HOH . I 7 HOH H 155 1379 1379 HOH HOH . I 7 HOH H 156 1380 1380 HOH HOH . I 7 HOH H 157 1381 1381 HOH HOH . I 7 HOH H 158 1382 1382 HOH HOH . I 7 HOH H 159 1383 1383 HOH HOH . I 7 HOH H 160 1384 1384 HOH HOH . I 7 HOH H 161 1385 1385 HOH HOH . I 7 HOH H 162 1386 1386 HOH HOH . I 7 HOH H 163 1387 1387 HOH HOH . I 7 HOH H 164 1388 1388 HOH HOH . I 7 HOH H 165 1390 1390 HOH HOH . I 7 HOH H 166 1391 1391 HOH HOH . I 7 HOH H 167 1393 1393 HOH HOH . I 7 HOH H 168 1395 1395 HOH HOH . I 7 HOH H 169 1396 1396 HOH HOH . I 7 HOH H 170 1397 1397 HOH HOH . I 7 HOH H 171 1398 1398 HOH HOH . I 7 HOH H 172 1399 1399 HOH HOH . I 7 HOH H 173 1400 1400 HOH HOH . I 7 HOH H 174 1401 1401 HOH HOH . I 7 HOH H 175 1402 1402 HOH HOH . I 7 HOH H 176 1403 1403 HOH HOH . I 7 HOH H 177 1404 1404 HOH HOH . I 7 HOH H 178 1405 1405 HOH HOH . I 7 HOH H 179 1406 1406 HOH HOH . I 7 HOH H 180 1407 1407 HOH HOH . I 7 HOH H 181 1408 1408 HOH HOH . I 7 HOH H 182 1409 1409 HOH HOH . I 7 HOH H 183 1410 1410 HOH HOH . I 7 HOH H 184 1412 1412 HOH HOH . I 7 HOH H 185 1413 1413 HOH HOH . I 7 HOH H 186 1414 1414 HOH HOH . I 7 HOH H 187 1416 1416 HOH HOH . I 7 HOH H 188 1417 1417 HOH HOH . I 7 HOH H 189 1418 1418 HOH HOH . I 7 HOH H 190 1419 1419 HOH HOH . I 7 HOH H 191 1420 1420 HOH HOH . I 7 HOH H 192 1421 1421 HOH HOH . I 7 HOH H 193 1422 1422 HOH HOH . I 7 HOH H 194 1424 1424 HOH HOH . I 7 HOH H 195 1425 1425 HOH HOH . I 7 HOH H 196 1426 1426 HOH HOH . I 7 HOH H 197 1428 1428 HOH HOH . I 7 HOH H 198 1430 1430 HOH HOH . I 7 HOH H 199 1431 1431 HOH HOH . I 7 HOH H 200 1432 1432 HOH HOH . I 7 HOH H 201 1433 1433 HOH HOH . I 7 HOH H 202 1434 1434 HOH HOH . I 7 HOH H 203 1435 1435 HOH HOH . I 7 HOH H 204 1436 1436 HOH HOH . I 7 HOH H 205 1437 1437 HOH HOH . I 7 HOH H 206 1438 1438 HOH HOH . I 7 HOH H 207 1442 1442 HOH HOH . I 7 HOH H 208 1443 1443 HOH HOH . I 7 HOH H 209 1445 1445 HOH HOH . I 7 HOH H 210 1446 1446 HOH HOH . I 7 HOH H 211 1448 1448 HOH HOH . I 7 HOH H 212 1449 1449 HOH HOH . I 7 HOH H 213 1450 1450 HOH HOH . I 7 HOH H 214 1451 1451 HOH HOH . I 7 HOH H 215 1452 1452 HOH HOH . I 7 HOH H 216 1454 1454 HOH HOH . I 7 HOH H 217 1455 1455 HOH HOH . I 7 HOH H 218 1456 1456 HOH HOH . I 7 HOH H 219 1458 1458 HOH HOH . I 7 HOH H 220 1459 1459 HOH HOH . I 7 HOH H 221 1461 1461 HOH HOH . I 7 HOH H 222 1463 1463 HOH HOH . I 7 HOH H 223 1465 1465 HOH HOH . I 7 HOH H 224 1466 1466 HOH HOH . I 7 HOH H 225 1467 1467 HOH HOH . I 7 HOH H 226 1468 1468 HOH HOH . I 7 HOH H 227 1469 1469 HOH HOH . I 7 HOH H 228 1470 1470 HOH HOH . I 7 HOH H 229 1471 1471 HOH HOH . I 7 HOH H 230 1472 1472 HOH HOH . J 7 HOH I 1 1334 1334 HOH HOH . J 7 HOH I 2 1356 1356 HOH HOH . J 7 HOH I 3 1394 1394 HOH HOH . J 7 HOH I 4 1439 1439 HOH HOH . J 7 HOH I 5 1440 1440 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 4 _atom_site.Cartn_x 5.537 _atom_site.Cartn_y -13.086 _atom_site.Cartn_z 30.488 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 15.13 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1100 _atom_site.auth_asym_id H _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #