data_1PK7 # _model_server_result.job_id ih93EKxjktyB5B9bSdPEhA _model_server_result.datetime_utc '2024-11-27 21:23:18' _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 1pk7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1247}' # _entry.id 1PK7 # _exptl.entry_id 1PK7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 1PK7 _cell.length_a 121.8 _cell.length_b 121.8 _cell.length_c 242 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PK7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,K,L _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' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 40.333333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I N N # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 1PK7 _atom_sites.fract_transf_matrix[1][1] 0.00821 _atom_sites.fract_transf_matrix[1][2] 0.00474 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00948 _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] 0.004132 _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 2 PO4 A 1 1248 247 PO4 PO4 . E 3 ADN A 1 1245 245 ADN ADN . F 2 PO4 B 1 1249 247 PO4 PO4 . G 3 ADN B 1 1246 245 ADN ADN . H 2 PO4 C 1 1250 247 PO4 PO4 . I 3 ADN C 1 1247 245 ADN ADN . J 4 HOH A 1 1249 8 HOH WAT . J 4 HOH A 2 1250 21 HOH WAT . J 4 HOH A 3 1251 22 HOH WAT . J 4 HOH A 4 1252 44 HOH WAT . J 4 HOH A 5 1253 46 HOH WAT . J 4 HOH A 6 1254 51 HOH WAT . J 4 HOH A 7 1255 53 HOH WAT . J 4 HOH A 8 1256 55 HOH WAT . J 4 HOH A 9 1257 57 HOH WAT . J 4 HOH A 10 1258 58 HOH WAT . J 4 HOH A 11 1259 64 HOH WAT . J 4 HOH A 12 1260 69 HOH WAT . J 4 HOH A 13 1261 71 HOH WAT . J 4 HOH A 14 1262 74 HOH WAT . J 4 HOH A 15 1263 78 HOH WAT . J 4 HOH A 16 1264 81 HOH WAT . J 4 HOH A 17 1265 83 HOH WAT . J 4 HOH A 18 1266 87 HOH WAT . J 4 HOH A 19 1267 90 HOH WAT . J 4 HOH A 20 1268 96 HOH WAT . J 4 HOH A 21 1269 97 HOH WAT . J 4 HOH A 22 1270 104 HOH WAT . J 4 HOH A 23 1271 111 HOH WAT . J 4 HOH A 24 1272 114 HOH WAT . J 4 HOH A 25 1273 115 HOH WAT . J 4 HOH A 26 1274 119 HOH WAT . J 4 HOH A 27 1275 120 HOH WAT . J 4 HOH A 28 1276 122 HOH WAT . J 4 HOH A 29 1277 125 HOH WAT . J 4 HOH A 30 1278 129 HOH WAT . J 4 HOH A 31 1279 130 HOH WAT . J 4 HOH A 32 1280 131 HOH WAT . J 4 HOH A 33 1281 133 HOH WAT . J 4 HOH A 34 1282 135 HOH WAT . J 4 HOH A 35 1283 137 HOH WAT . J 4 HOH A 36 1284 138 HOH WAT . J 4 HOH A 37 1285 140 HOH WAT . J 4 HOH A 38 1286 143 HOH WAT . J 4 HOH A 39 1287 145 HOH WAT . J 4 HOH A 40 1288 147 HOH WAT . J 4 HOH A 41 1289 149 HOH WAT . J 4 HOH A 42 1290 156 HOH WAT . J 4 HOH A 43 1291 160 HOH WAT . J 4 HOH A 44 1292 164 HOH WAT . J 4 HOH A 45 1293 168 HOH WAT . J 4 HOH A 46 1294 169 HOH WAT . J 4 HOH A 47 1295 170 HOH WAT . J 4 HOH A 48 1296 171 HOH WAT . J 4 HOH A 49 1297 186 HOH WAT . J 4 HOH A 50 1298 187 HOH WAT . J 4 HOH A 51 1299 188 HOH WAT . J 4 HOH A 52 1300 190 HOH WAT . J 4 HOH A 53 1301 191 HOH WAT . J 4 HOH A 54 1302 192 HOH WAT . J 4 HOH A 55 1303 202 HOH WAT . J 4 HOH A 56 1304 206 HOH WAT . J 4 HOH A 57 1305 207 HOH WAT . J 4 HOH A 58 1306 208 HOH WAT . J 4 HOH A 59 1307 210 HOH WAT . J 4 HOH A 60 1308 217 HOH WAT . J 4 HOH A 61 1309 226 HOH WAT . J 4 HOH A 62 1310 229 HOH WAT . J 4 HOH A 63 1311 232 HOH WAT . J 4 HOH A 64 1312 236 HOH WAT . J 4 HOH A 65 1313 241 HOH WAT . J 4 HOH A 66 1314 242 HOH WAT . J 4 HOH A 67 1315 246 HOH WAT . J 4 HOH A 68 1316 249 HOH WAT . J 4 HOH A 69 1317 251 HOH WAT . J 4 HOH A 70 1318 252 HOH WAT . J 4 HOH A 71 1319 256 HOH WAT . J 4 HOH A 72 1320 257 HOH WAT . J 4 HOH A 73 1321 260 HOH WAT . J 4 HOH A 74 1322 261 HOH WAT . J 4 HOH A 75 1323 266 HOH WAT . J 4 HOH A 76 1324 272 HOH WAT . J 4 HOH A 77 1325 277 HOH WAT . J 4 HOH A 78 1326 278 HOH WAT . K 4 HOH B 1 1250 5 HOH WAT . K 4 HOH B 2 1251 10 HOH WAT . K 4 HOH B 3 1252 12 HOH WAT . K 4 HOH B 4 1253 13 HOH WAT . K 4 HOH B 5 1254 14 HOH WAT . K 4 HOH B 6 1255 15 HOH WAT . K 4 HOH B 7 1256 16 HOH WAT . K 4 HOH B 8 1257 17 HOH WAT . K 4 HOH B 9 1258 18 HOH WAT . K 4 HOH B 10 1259 19 HOH WAT . K 4 HOH B 11 1260 20 HOH WAT . K 4 HOH B 12 1261 23 HOH WAT . K 4 HOH B 13 1262 25 HOH WAT . K 4 HOH B 14 1263 26 HOH WAT . K 4 HOH B 15 1264 27 HOH WAT . K 4 HOH B 16 1265 29 HOH WAT . K 4 HOH B 17 1266 30 HOH WAT . K 4 HOH B 18 1267 31 HOH WAT . K 4 HOH B 19 1268 33 HOH WAT . K 4 HOH B 20 1269 35 HOH WAT . K 4 HOH B 21 1270 37 HOH WAT . K 4 HOH B 22 1271 39 HOH WAT . K 4 HOH B 23 1272 41 HOH WAT . K 4 HOH B 24 1273 43 HOH WAT . K 4 HOH B 25 1274 47 HOH WAT . K 4 HOH B 26 1275 48 HOH WAT . K 4 HOH B 27 1276 52 HOH WAT . K 4 HOH B 28 1277 59 HOH WAT . K 4 HOH B 29 1278 60 HOH WAT . K 4 HOH B 30 1279 61 HOH WAT . K 4 HOH B 31 1280 62 HOH WAT . K 4 HOH B 32 1281 66 HOH WAT . K 4 HOH B 33 1282 67 HOH WAT . K 4 HOH B 34 1283 68 HOH WAT . K 4 HOH B 35 1284 70 HOH WAT . K 4 HOH B 36 1285 72 HOH WAT . K 4 HOH B 37 1286 75 HOH WAT . K 4 HOH B 38 1287 77 HOH WAT . K 4 HOH B 39 1288 79 HOH WAT . K 4 HOH B 40 1289 86 HOH WAT . K 4 HOH B 41 1290 88 HOH WAT . K 4 HOH B 42 1291 92 HOH WAT . K 4 HOH B 43 1292 93 HOH WAT . K 4 HOH B 44 1293 94 HOH WAT . K 4 HOH B 45 1294 95 HOH WAT . K 4 HOH B 46 1295 99 HOH WAT . K 4 HOH B 47 1296 102 HOH WAT . K 4 HOH B 48 1297 103 HOH WAT . K 4 HOH B 49 1298 107 HOH WAT . K 4 HOH B 50 1299 108 HOH WAT . K 4 HOH B 51 1300 110 HOH WAT . K 4 HOH B 52 1301 113 HOH WAT . K 4 HOH B 53 1302 117 HOH WAT . K 4 HOH B 54 1303 124 HOH WAT . K 4 HOH B 55 1304 128 HOH WAT . K 4 HOH B 56 1305 136 HOH WAT . K 4 HOH B 57 1306 141 HOH WAT . K 4 HOH B 58 1307 148 HOH WAT . K 4 HOH B 59 1308 150 HOH WAT . K 4 HOH B 60 1309 151 HOH WAT . K 4 HOH B 61 1310 152 HOH WAT . K 4 HOH B 62 1311 155 HOH WAT . K 4 HOH B 63 1312 158 HOH WAT . K 4 HOH B 64 1313 159 HOH WAT . K 4 HOH B 65 1314 162 HOH WAT . K 4 HOH B 66 1315 165 HOH WAT . K 4 HOH B 67 1316 173 HOH WAT . K 4 HOH B 68 1317 177 HOH WAT . K 4 HOH B 69 1318 182 HOH WAT . K 4 HOH B 70 1319 185 HOH WAT . K 4 HOH B 71 1320 189 HOH WAT . K 4 HOH B 72 1321 197 HOH WAT . K 4 HOH B 73 1322 200 HOH WAT . K 4 HOH B 74 1323 201 HOH WAT . K 4 HOH B 75 1324 211 HOH WAT . K 4 HOH B 76 1325 212 HOH WAT . K 4 HOH B 77 1326 218 HOH WAT . K 4 HOH B 78 1327 220 HOH WAT . K 4 HOH B 79 1328 221 HOH WAT . K 4 HOH B 80 1329 227 HOH WAT . K 4 HOH B 81 1330 228 HOH WAT . K 4 HOH B 82 1331 231 HOH WAT . K 4 HOH B 83 1332 239 HOH WAT . K 4 HOH B 84 1333 240 HOH WAT . K 4 HOH B 85 1334 245 HOH WAT . K 4 HOH B 86 1335 247 HOH WAT . K 4 HOH B 87 1336 253 HOH WAT . K 4 HOH B 88 1337 258 HOH WAT . K 4 HOH B 89 1338 259 HOH WAT . K 4 HOH B 90 1339 262 HOH WAT . K 4 HOH B 91 1340 267 HOH WAT . K 4 HOH B 92 1341 270 HOH WAT . K 4 HOH B 93 1342 274 HOH WAT . K 4 HOH B 94 1343 279 HOH WAT . K 4 HOH B 95 1344 281 HOH WAT . K 4 HOH B 96 1345 282 HOH WAT . K 4 HOH B 97 1346 283 HOH WAT . L 4 HOH C 1 1251 4 HOH WAT . L 4 HOH C 2 1252 6 HOH WAT . L 4 HOH C 3 1253 7 HOH WAT . L 4 HOH C 4 1254 9 HOH WAT . L 4 HOH C 5 1255 24 HOH WAT . L 4 HOH C 6 1256 28 HOH WAT . L 4 HOH C 7 1257 32 HOH WAT . L 4 HOH C 8 1258 36 HOH WAT . L 4 HOH C 9 1259 38 HOH WAT . L 4 HOH C 10 1260 40 HOH WAT . L 4 HOH C 11 1261 42 HOH WAT . L 4 HOH C 12 1262 45 HOH WAT . L 4 HOH C 13 1263 50 HOH WAT . L 4 HOH C 14 1264 54 HOH WAT . L 4 HOH C 15 1265 56 HOH WAT . L 4 HOH C 16 1266 73 HOH WAT . L 4 HOH C 17 1267 76 HOH WAT . L 4 HOH C 18 1268 80 HOH WAT . L 4 HOH C 19 1269 82 HOH WAT . L 4 HOH C 20 1270 84 HOH WAT . L 4 HOH C 21 1271 89 HOH WAT . L 4 HOH C 22 1272 91 HOH WAT . L 4 HOH C 23 1273 98 HOH WAT . L 4 HOH C 24 1274 100 HOH WAT . L 4 HOH C 25 1275 101 HOH WAT . L 4 HOH C 26 1276 105 HOH WAT . L 4 HOH C 27 1277 112 HOH WAT . L 4 HOH C 28 1278 116 HOH WAT . L 4 HOH C 29 1279 118 HOH WAT . L 4 HOH C 30 1280 121 HOH WAT . L 4 HOH C 31 1281 123 HOH WAT . L 4 HOH C 32 1282 134 HOH WAT . L 4 HOH C 33 1283 139 HOH WAT . L 4 HOH C 34 1284 142 HOH WAT . L 4 HOH C 35 1285 144 HOH WAT . L 4 HOH C 36 1286 146 HOH WAT . L 4 HOH C 37 1287 153 HOH WAT . L 4 HOH C 38 1288 154 HOH WAT . L 4 HOH C 39 1289 157 HOH WAT . L 4 HOH C 40 1290 161 HOH WAT . L 4 HOH C 41 1291 163 HOH WAT . L 4 HOH C 42 1292 167 HOH WAT . L 4 HOH C 43 1293 172 HOH WAT . L 4 HOH C 44 1294 174 HOH WAT . L 4 HOH C 45 1295 175 HOH WAT . L 4 HOH C 46 1296 176 HOH WAT . L 4 HOH C 47 1297 178 HOH WAT . L 4 HOH C 48 1298 179 HOH WAT . L 4 HOH C 49 1299 181 HOH WAT . L 4 HOH C 50 1300 183 HOH WAT . L 4 HOH C 51 1301 184 HOH WAT . L 4 HOH C 52 1302 193 HOH WAT . L 4 HOH C 53 1303 194 HOH WAT . L 4 HOH C 54 1304 195 HOH WAT . L 4 HOH C 55 1305 196 HOH WAT . L 4 HOH C 56 1306 203 HOH WAT . L 4 HOH C 57 1307 204 HOH WAT . L 4 HOH C 58 1308 209 HOH WAT . L 4 HOH C 59 1309 214 HOH WAT . L 4 HOH C 60 1310 215 HOH WAT . L 4 HOH C 61 1311 216 HOH WAT . L 4 HOH C 62 1312 222 HOH WAT . L 4 HOH C 63 1313 223 HOH WAT . L 4 HOH C 64 1314 224 HOH WAT . L 4 HOH C 65 1315 225 HOH WAT . L 4 HOH C 66 1316 233 HOH WAT . L 4 HOH C 67 1317 237 HOH WAT . L 4 HOH C 68 1318 238 HOH WAT . L 4 HOH C 69 1319 243 HOH WAT . L 4 HOH C 70 1320 248 HOH WAT . L 4 HOH C 71 1321 254 HOH WAT . L 4 HOH C 72 1322 255 HOH WAT . L 4 HOH C 73 1323 263 HOH WAT . L 4 HOH C 74 1324 264 HOH WAT . L 4 HOH C 75 1325 265 HOH WAT . L 4 HOH C 76 1326 268 HOH WAT . L 4 HOH C 77 1327 269 HOH WAT . L 4 HOH C 78 1328 273 HOH WAT . L 4 HOH C 79 1329 275 HOH WAT . L 4 HOH C 80 1330 276 HOH WAT . # 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 O O5' ADN . . . I 3 51.088 53.202 30.542 1 60.32 ? O5' ADN 1247 C 1 HETATM 2 C C5' ADN . . . I 3 52.085 52.195 30.456 1 59.98 ? C5' ADN 1247 C 1 HETATM 3 C C4' ADN . . . I 3 51.507 50.836 30.843 1 60.18 ? C4' ADN 1247 C 1 HETATM 4 O O4' ADN . . . I 3 50.405 50.43 30.014 1 61.01 ? O4' ADN 1247 C 1 HETATM 5 C C3' ADN . . . I 3 52.485 49.689 30.771 1 60.38 ? C3' ADN 1247 C 1 HETATM 6 O O3' ADN . . . I 3 52.104 48.758 31.785 1 59.21 ? O3' ADN 1247 C 1 HETATM 7 C C2' ADN . . . I 3 52.276 49.179 29.316 1 61.56 ? C2' ADN 1247 C 1 HETATM 8 O O2' ADN . . . I 3 52.144 47.76 29.246 1 63.07 ? O2' ADN 1247 C 1 HETATM 9 C C1' ADN . . . I 3 50.91 49.714 28.857 1 61.16 ? C1' ADN 1247 C 1 HETATM 10 N N9 ADN . . . I 3 50.78 50.562 27.602 1 60.3 ? N9 ADN 1247 C 1 HETATM 11 C C8 ADN . . . I 3 49.575 51.087 27.117 1 59.42 ? C8 ADN 1247 C 1 HETATM 12 N N7 ADN . . . I 3 49.777 51.811 25.973 1 59.07 ? N7 ADN 1247 C 1 HETATM 13 C C5 ADN . . . I 3 51.107 51.751 25.722 1 58.24 ? C5 ADN 1247 C 1 HETATM 14 C C6 ADN . . . I 3 51.787 52.357 24.638 1 57.08 ? C6 ADN 1247 C 1 HETATM 15 N N6 ADN . . . I 3 51.226 53.091 23.68 1 57.48 ? N6 ADN 1247 C 1 HETATM 16 N N1 ADN . . . I 3 53.139 52.137 24.623 1 55.37 ? N1 ADN 1247 C 1 HETATM 17 C C2 ADN . . . I 3 53.732 51.393 25.589 1 55.96 ? C2 ADN 1247 C 1 HETATM 18 N N3 ADN . . . I 3 53.14 50.785 26.657 1 57.17 ? N3 ADN 1247 C 1 HETATM 19 C C4 ADN . . . I 3 51.775 51.008 26.669 1 58.52 ? C4 ADN 1247 C 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #