data_4YC9
#
_model_server_result.job_id            20S_bgY80LCJvglDf1d6-Q 
_model_server_result.datetime_utc      '2025-01-11 05:55:12' 
_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          4yc9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1103}' 
#
_entry.id    4YC9 
#
_exptl.entry_id    4YC9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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          112.07 
_cell.angle_gamma         90 
_cell.entry_id            4YC9 
_cell.length_a            89.839 
_cell.length_b            35.624 
_cell.length_c            65.367 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YC9 
_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    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 
_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                      3 
_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
metalc ? metalc1 A SG CYS 7 A CYS 829 1_555 B ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc2 A SG CYS 10 A CYS 832 1_555 B ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc3 A SG CYS 19 A CYS 841 1_555 C ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc4 A SG CYS 22 A CYS 844 1_555 C ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc5 A ND1 HIS 27 A HIS 849 1_555 B ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc6 A SG CYS 30 A CYS 852 1_555 B ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc7 A SG CYS 45 A CYS 867 1_555 C ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? 
metalc ? metalc8 A SG CYS 48 A CYS 870 1_555 C ZN ZN . A ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
#
_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 219 n n 
C1 C2 GOL sing 220 n n 
C1 H11 GOL sing 221 n n 
C1 H12 GOL sing 222 n n 
O1 HO1 GOL sing 223 n n 
C2 O2 GOL sing 224 n n 
C2 C3 GOL sing 225 n n 
C2 H2 GOL sing 226 n n 
O2 HO2 GOL sing 227 n n 
C3 O3 GOL sing 228 n n 
C3 H31 GOL sing 229 n n 
C3 H32 GOL sing 230 n n 
O3 HO3 GOL sing 231 n n 
#
_atom_sites.entry_id                     4YC9 
_atom_sites.fract_transf_matrix[1][1]    0.011131 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004513 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.028071 
_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]    0.016508 
_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 1101 1 ZN ZN . 
C 2 ZN A 1 1102 2 ZN ZN . 
D 3 GOL A 1 1103 3 GOL GOL . 
E 4 4C1 A 1 1104 4 4C1 571 . 
F 5 HOH A 1 1201 213 HOH HOH . 
F 5 HOH A 2 1202 76 HOH HOH . 
F 5 HOH A 3 1203 142 HOH HOH . 
F 5 HOH A 4 1204 177 HOH HOH . 
F 5 HOH A 5 1205 111 HOH HOH . 
F 5 HOH A 6 1206 98 HOH HOH . 
F 5 HOH A 7 1207 185 HOH HOH . 
F 5 HOH A 8 1208 11 HOH HOH . 
F 5 HOH A 9 1209 153 HOH HOH . 
F 5 HOH A 10 1210 198 HOH HOH . 
F 5 HOH A 11 1211 86 HOH HOH . 
F 5 HOH A 12 1212 183 HOH HOH . 
F 5 HOH A 13 1213 38 HOH HOH . 
F 5 HOH A 14 1214 179 HOH HOH . 
F 5 HOH A 15 1215 79 HOH HOH . 
F 5 HOH A 16 1216 166 HOH HOH . 
F 5 HOH A 17 1217 31 HOH HOH . 
F 5 HOH A 18 1218 32 HOH HOH . 
F 5 HOH A 19 1219 170 HOH HOH . 
F 5 HOH A 20 1220 59 HOH HOH . 
F 5 HOH A 21 1221 104 HOH HOH . 
F 5 HOH A 22 1222 30 HOH HOH . 
F 5 HOH A 23 1223 94 HOH HOH . 
F 5 HOH A 24 1224 172 HOH HOH . 
F 5 HOH A 25 1225 121 HOH HOH . 
F 5 HOH A 26 1226 44 HOH HOH . 
F 5 HOH A 27 1227 202 HOH HOH . 
F 5 HOH A 28 1228 5 HOH HOH . 
F 5 HOH A 29 1229 80 HOH HOH . 
F 5 HOH A 30 1230 53 HOH HOH . 
F 5 HOH A 31 1231 77 HOH HOH . 
F 5 HOH A 32 1232 67 HOH HOH . 
F 5 HOH A 33 1233 16 HOH HOH . 
F 5 HOH A 34 1234 92 HOH HOH . 
F 5 HOH A 35 1235 95 HOH HOH . 
F 5 HOH A 36 1236 82 HOH HOH . 
F 5 HOH A 37 1237 88 HOH HOH . 
F 5 HOH A 38 1238 74 HOH HOH . 
F 5 HOH A 39 1239 83 HOH HOH . 
F 5 HOH A 40 1240 163 HOH HOH . 
F 5 HOH A 41 1241 90 HOH HOH . 
F 5 HOH A 42 1242 165 HOH HOH . 
F 5 HOH A 43 1243 26 HOH HOH . 
F 5 HOH A 44 1244 97 HOH HOH . 
F 5 HOH A 45 1245 34 HOH HOH . 
F 5 HOH A 46 1246 41 HOH HOH . 
F 5 HOH A 47 1247 216 HOH HOH . 
F 5 HOH A 48 1248 18 HOH HOH . 
F 5 HOH A 49 1249 123 HOH HOH . 
F 5 HOH A 50 1250 65 HOH HOH . 
F 5 HOH A 51 1251 133 HOH HOH . 
F 5 HOH A 52 1252 68 HOH HOH . 
F 5 HOH A 53 1253 96 HOH HOH . 
F 5 HOH A 54 1254 154 HOH HOH . 
F 5 HOH A 55 1255 136 HOH HOH . 
F 5 HOH A 56 1256 141 HOH HOH . 
F 5 HOH A 57 1257 149 HOH HOH . 
F 5 HOH A 58 1258 139 HOH HOH . 
F 5 HOH A 59 1259 176 HOH HOH . 
F 5 HOH A 60 1260 114 HOH HOH . 
F 5 HOH A 61 1261 100 HOH HOH . 
F 5 HOH A 62 1262 215 HOH HOH . 
F 5 HOH A 63 1263 152 HOH HOH . 
F 5 HOH A 64 1264 54 HOH HOH . 
F 5 HOH A 65 1265 150 HOH HOH . 
F 5 HOH A 66 1266 168 HOH HOH . 
F 5 HOH A 67 1267 174 HOH HOH . 
F 5 HOH A 68 1268 158 HOH HOH . 
F 5 HOH A 69 1269 162 HOH HOH . 
F 5 HOH A 70 1270 93 HOH HOH . 
F 5 HOH A 71 1271 60 HOH HOH . 
F 5 HOH A 72 1272 72 HOH HOH . 
F 5 HOH A 73 1273 214 HOH HOH . 
F 5 HOH A 74 1274 89 HOH HOH . 
F 5 HOH A 75 1275 130 HOH HOH . 
F 5 HOH A 76 1276 171 HOH HOH . 
F 5 HOH A 77 1277 160 HOH HOH . 
F 5 HOH A 78 1278 117 HOH HOH . 
F 5 HOH A 79 1279 180 HOH HOH . 
F 5 HOH A 80 1280 105 HOH HOH . 
F 5 HOH A 81 1281 33 HOH HOH . 
F 5 HOH A 82 1282 146 HOH HOH . 
F 5 HOH A 83 1283 64 HOH HOH . 
F 5 HOH A 84 1284 169 HOH HOH . 
F 5 HOH A 85 1285 140 HOH HOH . 
F 5 HOH A 86 1286 200 HOH HOH . 
F 5 HOH A 87 1287 6 HOH HOH . 
F 5 HOH A 88 1288 7 HOH HOH . 
F 5 HOH A 89 1289 8 HOH HOH . 
F 5 HOH A 90 1290 9 HOH HOH . 
F 5 HOH A 91 1291 10 HOH HOH . 
F 5 HOH A 92 1292 12 HOH HOH . 
F 5 HOH A 93 1293 13 HOH HOH . 
F 5 HOH A 94 1294 14 HOH HOH . 
F 5 HOH A 95 1295 15 HOH HOH . 
F 5 HOH A 96 1296 17 HOH HOH . 
F 5 HOH A 97 1297 19 HOH HOH . 
F 5 HOH A 98 1298 20 HOH HOH . 
F 5 HOH A 99 1299 21 HOH HOH . 
F 5 HOH A 100 1300 22 HOH HOH . 
F 5 HOH A 101 1301 23 HOH HOH . 
F 5 HOH A 102 1302 24 HOH HOH . 
F 5 HOH A 103 1303 25 HOH HOH . 
F 5 HOH A 104 1304 27 HOH HOH . 
F 5 HOH A 105 1305 28 HOH HOH . 
F 5 HOH A 106 1306 29 HOH HOH . 
F 5 HOH A 107 1307 35 HOH HOH . 
F 5 HOH A 108 1308 36 HOH HOH . 
F 5 HOH A 109 1309 37 HOH HOH . 
F 5 HOH A 110 1310 39 HOH HOH . 
F 5 HOH A 111 1311 40 HOH HOH . 
F 5 HOH A 112 1312 42 HOH HOH . 
F 5 HOH A 113 1313 43 HOH HOH . 
F 5 HOH A 114 1314 45 HOH HOH . 
F 5 HOH A 115 1315 46 HOH HOH . 
F 5 HOH A 116 1316 47 HOH HOH . 
F 5 HOH A 117 1317 48 HOH HOH . 
F 5 HOH A 118 1318 49 HOH HOH . 
F 5 HOH A 119 1319 50 HOH HOH . 
F 5 HOH A 120 1320 51 HOH HOH . 
F 5 HOH A 121 1321 52 HOH HOH . 
F 5 HOH A 122 1322 55 HOH HOH . 
F 5 HOH A 123 1323 56 HOH HOH . 
F 5 HOH A 124 1324 57 HOH HOH . 
F 5 HOH A 125 1325 58 HOH HOH . 
F 5 HOH A 126 1326 61 HOH HOH . 
F 5 HOH A 127 1327 62 HOH HOH . 
F 5 HOH A 128 1328 63 HOH HOH . 
F 5 HOH A 129 1329 66 HOH HOH . 
F 5 HOH A 130 1330 69 HOH HOH . 
F 5 HOH A 131 1331 70 HOH HOH . 
F 5 HOH A 132 1332 71 HOH HOH . 
F 5 HOH A 133 1333 73 HOH HOH . 
F 5 HOH A 134 1334 75 HOH HOH . 
F 5 HOH A 135 1335 78 HOH HOH . 
F 5 HOH A 136 1336 81 HOH HOH . 
F 5 HOH A 137 1337 84 HOH HOH . 
F 5 HOH A 138 1338 85 HOH HOH . 
F 5 HOH A 139 1339 87 HOH HOH . 
F 5 HOH A 140 1340 91 HOH HOH . 
F 5 HOH A 141 1341 99 HOH HOH . 
F 5 HOH A 142 1342 101 HOH HOH . 
F 5 HOH A 143 1343 102 HOH HOH . 
F 5 HOH A 144 1344 103 HOH HOH . 
F 5 HOH A 145 1345 106 HOH HOH . 
F 5 HOH A 146 1346 107 HOH HOH . 
F 5 HOH A 147 1347 108 HOH HOH . 
F 5 HOH A 148 1348 109 HOH HOH . 
F 5 HOH A 149 1349 110 HOH HOH . 
F 5 HOH A 150 1350 112 HOH HOH . 
F 5 HOH A 151 1351 113 HOH HOH . 
F 5 HOH A 152 1352 115 HOH HOH . 
F 5 HOH A 153 1353 116 HOH HOH . 
F 5 HOH A 154 1354 118 HOH HOH . 
F 5 HOH A 155 1355 119 HOH HOH . 
F 5 HOH A 156 1356 120 HOH HOH . 
F 5 HOH A 157 1357 122 HOH HOH . 
F 5 HOH A 158 1358 124 HOH HOH . 
F 5 HOH A 159 1359 125 HOH HOH . 
F 5 HOH A 160 1360 126 HOH HOH . 
F 5 HOH A 161 1361 127 HOH HOH . 
F 5 HOH A 162 1362 128 HOH HOH . 
F 5 HOH A 163 1363 129 HOH HOH . 
F 5 HOH A 164 1364 131 HOH HOH . 
F 5 HOH A 165 1365 132 HOH HOH . 
F 5 HOH A 166 1366 134 HOH HOH . 
F 5 HOH A 167 1367 135 HOH HOH . 
F 5 HOH A 168 1368 137 HOH HOH . 
F 5 HOH A 169 1369 138 HOH HOH . 
F 5 HOH A 170 1370 143 HOH HOH . 
F 5 HOH A 171 1371 144 HOH HOH . 
F 5 HOH A 172 1372 145 HOH HOH . 
F 5 HOH A 173 1373 147 HOH HOH . 
F 5 HOH A 174 1374 148 HOH HOH . 
F 5 HOH A 175 1375 151 HOH HOH . 
F 5 HOH A 176 1376 155 HOH HOH . 
F 5 HOH A 177 1377 156 HOH HOH . 
F 5 HOH A 178 1378 157 HOH HOH . 
F 5 HOH A 179 1379 159 HOH HOH . 
F 5 HOH A 180 1380 161 HOH HOH . 
F 5 HOH A 181 1381 164 HOH HOH . 
F 5 HOH A 182 1382 167 HOH HOH . 
F 5 HOH A 183 1383 173 HOH HOH . 
F 5 HOH A 184 1384 175 HOH HOH . 
F 5 HOH A 185 1385 178 HOH HOH . 
F 5 HOH A 186 1386 181 HOH HOH . 
F 5 HOH A 187 1387 182 HOH HOH . 
F 5 HOH A 188 1388 184 HOH HOH . 
F 5 HOH A 189 1389 186 HOH HOH . 
F 5 HOH A 190 1390 187 HOH HOH . 
F 5 HOH A 191 1391 188 HOH HOH . 
F 5 HOH A 192 1392 189 HOH HOH . 
F 5 HOH A 193 1393 190 HOH HOH . 
F 5 HOH A 194 1394 191 HOH HOH . 
F 5 HOH A 195 1395 192 HOH HOH . 
F 5 HOH A 196 1396 193 HOH HOH . 
F 5 HOH A 197 1397 194 HOH HOH . 
F 5 HOH A 198 1398 195 HOH HOH . 
F 5 HOH A 199 1399 196 HOH HOH . 
F 5 HOH A 200 1400 197 HOH HOH . 
F 5 HOH A 201 1401 199 HOH HOH . 
F 5 HOH A 202 1402 201 HOH HOH . 
F 5 HOH A 203 1403 203 HOH HOH . 
F 5 HOH A 204 1404 204 HOH HOH . 
F 5 HOH A 205 1405 205 HOH HOH . 
F 5 HOH A 206 1406 206 HOH HOH . 
F 5 HOH A 207 1407 207 HOH HOH . 
F 5 HOH A 208 1408 208 HOH HOH . 
F 5 HOH A 209 1409 209 HOH HOH . 
F 5 HOH A 210 1410 210 HOH HOH . 
F 5 HOH A 211 1411 211 HOH HOH . 
F 5 HOH A 212 1412 212 HOH HOH . 
F 5 HOH A 213 1413 217 HOH HOH . 
F 5 HOH A 214 1414 218 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 . . . D 3 24.155 10.908 10.62 1 60.12 ? C1 GOL 1103 A 1 
HETATM 2 O O1 GOL . . . D 3 24.531 10.529 9.302 1 66.68 ? O1 GOL 1103 A 1 
HETATM 3 C C2 GOL . . . D 3 22.657 10.713 10.912 1 61.98 ? C2 GOL 1103 A 1 
HETATM 4 O O2 GOL . . . D 3 22.506 9.519 11.675 1 80.12 ? O2 GOL 1103 A 1 
HETATM 5 C C3 GOL . . . D 3 21.977 11.812 11.742 1 64.37 ? C3 GOL 1103 A 1 
HETATM 6 O O3 GOL . . . D 3 21.385 11.288 12.952 1 61.1 ? O3 GOL 1103 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           6 
#