data_4ZYX
#
_model_server_result.job_id            WD7SmGcvK4L7NaJgrgRq4g 
_model_server_result.datetime_utc      '2024-11-22 22:36:46' 
_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          4zyx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1101}' 
#
_entry.id    4ZYX 
#
_exptl.entry_id    4ZYX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.16 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'GLYCINAMIDE RIBONUCLEOTIDE' 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            4ZYX 
_cell.length_a            75.328 
_cell.length_b            75.328 
_cell.length_c            100.856 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4ZYX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 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 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C7 H13 N2 O8 P -2' 
_chem_comp.formula_weight    284.16 
_chem_comp.id                GAR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'GLYCINAMIDE RIBONUCLEOTIDE' 
_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
C1 O6 GAR sing 140 n n 
C1 C2 GAR sing 141 n n 
C1 C5 GAR sing 142 n n 
C1 H1 GAR sing 143 n n 
O6 HO6 GAR sing 144 n n 
C2 O8 GAR sing 145 n n 
C2 C3 GAR sing 146 n n 
C2 H2 GAR sing 147 n n 
O8 HO8 GAR sing 148 n n 
C3 O4 GAR sing 149 n n 
C3 N19 GAR sing 150 n n 
C3 H3 GAR sing 151 n n 
O4 C5 GAR sing 152 n n 
C5 C10 GAR sing 153 n n 
C5 H5 GAR sing 154 n n 
C10 O12 GAR sing 155 n n 
C10 H101 GAR sing 156 n n 
C10 H102 GAR sing 157 n n 
O12 P15 GAR sing 158 n n 
N19 C21 GAR sing 159 n n 
N19 H19 GAR sing 160 n n 
C21 O22 GAR doub 161 n n 
C21 C23 GAR sing 162 n n 
C23 N24 GAR sing 163 n n 
C23 H231 GAR sing 164 n n 
C23 H232 GAR sing 165 n n 
N24 H241 GAR sing 166 n n 
N24 H242 GAR sing 167 n n 
P15 O16 GAR doub 168 n n 
P15 O17 GAR sing 169 n n 
P15 O18 GAR sing 170 n n 
#
_atom_sites.entry_id                     4ZYX 
_atom_sites.fract_transf_matrix[1][1]    0.013275 
_atom_sites.fract_transf_matrix[1][2]    0.007664 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015329 
_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]    0.009915 
_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 GAR A 1 1101 1016 GAR GAR . 
C 3 3YB A 1 1102 1017 3YB 3GD . 
D 4 HOH A 1 1201 133 HOH HOH . 
D 4 HOH A 2 1202 146 HOH HOH . 
D 4 HOH A 3 1203 96 HOH HOH . 
D 4 HOH A 4 1204 88 HOH HOH . 
D 4 HOH A 5 1205 134 HOH HOH . 
D 4 HOH A 6 1206 104 HOH HOH . 
D 4 HOH A 7 1207 16 HOH HOH . 
D 4 HOH A 8 1208 63 HOH HOH . 
D 4 HOH A 9 1209 79 HOH HOH . 
D 4 HOH A 10 1210 43 HOH HOH . 
D 4 HOH A 11 1211 172 HOH HOH . 
D 4 HOH A 12 1212 86 HOH HOH . 
D 4 HOH A 13 1213 51 HOH HOH . 
D 4 HOH A 14 1214 25 HOH HOH . 
D 4 HOH A 15 1215 106 HOH HOH . 
D 4 HOH A 16 1216 170 HOH HOH . 
D 4 HOH A 17 1217 102 HOH HOH . 
D 4 HOH A 18 1218 67 HOH HOH . 
D 4 HOH A 19 1219 184 HOH HOH . 
D 4 HOH A 20 1220 157 HOH HOH . 
D 4 HOH A 21 1221 75 HOH HOH . 
D 4 HOH A 22 1222 22 HOH HOH . 
D 4 HOH A 23 1223 10 HOH HOH . 
D 4 HOH A 24 1224 143 HOH HOH . 
D 4 HOH A 25 1225 105 HOH HOH . 
D 4 HOH A 26 1226 117 HOH HOH . 
D 4 HOH A 27 1227 7 HOH HOH . 
D 4 HOH A 28 1228 72 HOH HOH . 
D 4 HOH A 29 1229 167 HOH HOH . 
D 4 HOH A 30 1230 82 HOH HOH . 
D 4 HOH A 31 1231 3 HOH HOH . 
D 4 HOH A 32 1232 80 HOH HOH . 
D 4 HOH A 33 1233 21 HOH HOH . 
D 4 HOH A 34 1234 175 HOH HOH . 
D 4 HOH A 35 1235 98 HOH HOH . 
D 4 HOH A 36 1236 89 HOH HOH . 
D 4 HOH A 37 1237 36 HOH HOH . 
D 4 HOH A 38 1238 28 HOH HOH . 
D 4 HOH A 39 1239 141 HOH HOH . 
D 4 HOH A 40 1240 14 HOH HOH . 
D 4 HOH A 41 1241 155 HOH HOH . 
D 4 HOH A 42 1242 159 HOH HOH . 
D 4 HOH A 43 1243 188 HOH HOH . 
D 4 HOH A 44 1244 162 HOH HOH . 
D 4 HOH A 45 1245 56 HOH HOH . 
D 4 HOH A 46 1246 138 HOH HOH . 
D 4 HOH A 47 1247 23 HOH HOH . 
D 4 HOH A 48 1248 83 HOH HOH . 
D 4 HOH A 49 1249 62 HOH HOH . 
D 4 HOH A 50 1250 195 HOH HOH . 
D 4 HOH A 51 1251 191 HOH HOH . 
D 4 HOH A 52 1252 27 HOH HOH . 
D 4 HOH A 53 1253 65 HOH HOH . 
D 4 HOH A 54 1254 2 HOH HOH . 
D 4 HOH A 55 1255 31 HOH HOH . 
D 4 HOH A 56 1256 45 HOH HOH . 
D 4 HOH A 57 1257 160 HOH HOH . 
D 4 HOH A 58 1258 12 HOH HOH . 
D 4 HOH A 59 1259 61 HOH HOH . 
D 4 HOH A 60 1260 33 HOH HOH . 
D 4 HOH A 61 1261 57 HOH HOH . 
D 4 HOH A 62 1262 4 HOH HOH . 
D 4 HOH A 63 1263 201 HOH HOH . 
D 4 HOH A 64 1264 20 HOH HOH . 
D 4 HOH A 65 1265 108 HOH HOH . 
D 4 HOH A 66 1266 34 HOH HOH . 
D 4 HOH A 67 1267 48 HOH HOH . 
D 4 HOH A 68 1268 163 HOH HOH . 
D 4 HOH A 69 1269 120 HOH HOH . 
D 4 HOH A 70 1270 203 HOH HOH . 
D 4 HOH A 71 1271 30 HOH HOH . 
D 4 HOH A 72 1272 182 HOH HOH . 
D 4 HOH A 73 1273 180 HOH HOH . 
D 4 HOH A 74 1274 123 HOH HOH . 
D 4 HOH A 75 1275 46 HOH HOH . 
D 4 HOH A 76 1276 58 HOH HOH . 
D 4 HOH A 77 1277 50 HOH HOH . 
D 4 HOH A 78 1278 32 HOH HOH . 
D 4 HOH A 79 1279 6 HOH HOH . 
D 4 HOH A 80 1280 17 HOH HOH . 
D 4 HOH A 81 1281 18 HOH HOH . 
D 4 HOH A 82 1282 44 HOH HOH . 
D 4 HOH A 83 1283 145 HOH HOH . 
D 4 HOH A 84 1284 53 HOH HOH . 
D 4 HOH A 85 1285 153 HOH HOH . 
D 4 HOH A 86 1286 192 HOH HOH . 
D 4 HOH A 87 1287 131 HOH HOH . 
D 4 HOH A 88 1288 95 HOH HOH . 
D 4 HOH A 89 1289 26 HOH HOH . 
D 4 HOH A 90 1290 126 HOH HOH . 
D 4 HOH A 91 1291 202 HOH HOH . 
D 4 HOH A 92 1292 116 HOH HOH . 
D 4 HOH A 93 1293 1 HOH HOH . 
D 4 HOH A 94 1294 40 HOH HOH . 
D 4 HOH A 95 1295 59 HOH HOH . 
D 4 HOH A 96 1296 125 HOH HOH . 
D 4 HOH A 97 1297 158 HOH HOH . 
D 4 HOH A 98 1298 73 HOH HOH . 
D 4 HOH A 99 1299 171 HOH HOH . 
D 4 HOH A 100 1300 121 HOH HOH . 
D 4 HOH A 101 1301 130 HOH HOH . 
D 4 HOH A 102 1302 41 HOH HOH . 
D 4 HOH A 103 1303 76 HOH HOH . 
D 4 HOH A 104 1304 35 HOH HOH . 
D 4 HOH A 105 1305 11 HOH HOH . 
D 4 HOH A 106 1306 71 HOH HOH . 
D 4 HOH A 107 1307 8 HOH HOH . 
D 4 HOH A 108 1308 15 HOH HOH . 
D 4 HOH A 109 1309 69 HOH HOH . 
D 4 HOH A 110 1310 161 HOH HOH . 
D 4 HOH A 111 1311 198 HOH HOH . 
D 4 HOH A 112 1312 193 HOH HOH . 
D 4 HOH A 113 1313 194 HOH HOH . 
D 4 HOH A 114 1314 54 HOH HOH . 
D 4 HOH A 115 1315 97 HOH HOH . 
D 4 HOH A 116 1316 85 HOH HOH . 
D 4 HOH A 117 1317 81 HOH HOH . 
D 4 HOH A 118 1318 60 HOH HOH . 
D 4 HOH A 119 1319 84 HOH HOH . 
D 4 HOH A 120 1320 9 HOH HOH . 
D 4 HOH A 121 1321 109 HOH HOH . 
D 4 HOH A 122 1322 176 HOH HOH . 
D 4 HOH A 123 1323 29 HOH HOH . 
D 4 HOH A 124 1324 13 HOH HOH . 
D 4 HOH A 125 1325 38 HOH HOH . 
D 4 HOH A 126 1326 129 HOH HOH . 
D 4 HOH A 127 1327 122 HOH HOH . 
D 4 HOH A 128 1328 19 HOH HOH . 
D 4 HOH A 129 1329 5 HOH HOH . 
D 4 HOH A 130 1330 68 HOH HOH . 
D 4 HOH A 131 1331 200 HOH HOH . 
D 4 HOH A 132 1332 66 HOH HOH . 
D 4 HOH A 133 1333 37 HOH HOH . 
D 4 HOH A 134 1334 118 HOH HOH . 
D 4 HOH A 135 1335 94 HOH HOH . 
D 4 HOH A 136 1336 87 HOH HOH . 
D 4 HOH A 137 1337 64 HOH HOH . 
D 4 HOH A 138 1338 47 HOH HOH . 
D 4 HOH A 139 1339 166 HOH HOH . 
D 4 HOH A 140 1340 151 HOH HOH . 
D 4 HOH A 141 1341 181 HOH HOH . 
D 4 HOH A 142 1342 101 HOH HOH . 
D 4 HOH A 143 1343 196 HOH HOH . 
D 4 HOH A 144 1344 183 HOH HOH . 
D 4 HOH A 145 1345 127 HOH HOH . 
D 4 HOH A 146 1346 148 HOH HOH . 
D 4 HOH A 147 1347 136 HOH HOH . 
D 4 HOH A 148 1348 169 HOH HOH . 
D 4 HOH A 149 1349 179 HOH HOH . 
D 4 HOH A 150 1350 173 HOH HOH . 
D 4 HOH A 151 1351 144 HOH HOH . 
D 4 HOH A 152 1352 124 HOH HOH . 
D 4 HOH A 153 1353 149 HOH HOH . 
D 4 HOH A 154 1354 107 HOH HOH . 
D 4 HOH A 155 1355 174 HOH HOH . 
D 4 HOH A 156 1356 140 HOH HOH . 
D 4 HOH A 157 1357 189 HOH HOH . 
D 4 HOH A 158 1358 205 HOH HOH . 
D 4 HOH A 159 1359 154 HOH HOH . 
D 4 HOH A 160 1360 152 HOH HOH . 
D 4 HOH A 161 1361 132 HOH HOH . 
D 4 HOH A 162 1362 39 HOH HOH . 
D 4 HOH A 163 1363 112 HOH HOH . 
D 4 HOH A 164 1364 99 HOH HOH . 
D 4 HOH A 165 1365 135 HOH HOH . 
D 4 HOH A 166 1366 185 HOH HOH . 
D 4 HOH A 167 1367 74 HOH HOH . 
D 4 HOH A 168 1368 114 HOH HOH . 
D 4 HOH A 169 1369 178 HOH HOH . 
D 4 HOH A 170 1370 197 HOH HOH . 
D 4 HOH A 171 1371 100 HOH HOH . 
D 4 HOH A 172 1372 204 HOH HOH . 
D 4 HOH A 173 1373 199 HOH HOH . 
D 4 HOH A 174 1374 91 HOH HOH . 
D 4 HOH A 175 1375 139 HOH HOH . 
D 4 HOH A 176 1376 156 HOH HOH . 
D 4 HOH A 177 1377 150 HOH HOH . 
D 4 HOH A 178 1378 208 HOH HOH . 
D 4 HOH A 179 1379 90 HOH HOH . 
D 4 HOH A 180 1380 177 HOH HOH . 
D 4 HOH A 181 1381 92 HOH HOH . 
D 4 HOH A 182 1382 206 HOH HOH . 
D 4 HOH A 183 1383 24 HOH HOH . 
D 4 HOH A 184 1384 128 HOH HOH . 
D 4 HOH A 185 1385 207 HOH HOH . 
D 4 HOH A 186 1386 49 HOH HOH . 
D 4 HOH A 187 1387 111 HOH HOH . 
D 4 HOH A 188 1388 93 HOH HOH . 
D 4 HOH A 189 1389 77 HOH HOH . 
D 4 HOH A 190 1390 42 HOH HOH . 
D 4 HOH A 191 1391 119 HOH HOH . 
D 4 HOH A 192 1392 55 HOH HOH . 
D 4 HOH A 193 1393 165 HOH HOH . 
D 4 HOH A 194 1394 190 HOH HOH . 
D 4 HOH A 195 1395 52 HOH HOH . 
D 4 HOH A 196 1396 110 HOH HOH . 
D 4 HOH A 197 1397 168 HOH HOH . 
D 4 HOH A 198 1398 164 HOH HOH . 
D 4 HOH A 199 1399 70 HOH HOH . 
D 4 HOH A 200 1400 78 HOH HOH . 
D 4 HOH A 201 1401 147 HOH HOH . 
D 4 HOH A 202 1402 137 HOH HOH . 
D 4 HOH A 203 1403 186 HOH HOH . 
D 4 HOH A 204 1404 115 HOH HOH . 
D 4 HOH A 205 1405 103 HOH HOH . 
D 4 HOH A 206 1406 113 HOH HOH . 
D 4 HOH A 207 1407 187 HOH HOH . 
D 4 HOH A 208 1408 142 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 GAR . . . B 2 -34.268 16.805 14.987 0.76 15.29 ? C1 GAR 1101 A 1 
HETATM 2 O O6 GAR . . . B 2 -34.674 15.789 14.066 0.76 18.06 ? O6 GAR 1101 A 1 
HETATM 3 C C2 GAR . . . B 2 -33.266 16.241 15.968 0.76 14.61 ? C2 GAR 1101 A 1 
HETATM 4 O O8 GAR . . . B 2 -33.55 14.903 16.396 0.76 14.68 ? O8 GAR 1101 A 1 
HETATM 5 C C3 GAR . . . B 2 -31.974 16.31 15.173 0.76 14.21 ? C3 GAR 1101 A 1 
HETATM 6 O O4 GAR . . . B 2 -32.077 17.579 14.527 0.76 14.91 ? O4 GAR 1101 A 1 
HETATM 7 C C5 GAR . . . B 2 -33.455 17.839 14.229 0.76 13.78 ? C5 GAR 1101 A 1 
HETATM 8 C C10 GAR . . . B 2 -33.828 19.22 14.724 0.76 12.85 ? C10 GAR 1101 A 1 
HETATM 9 O O12 GAR . . . B 2 -35.119 19.566 14.241 0.76 11.97 ? O12 GAR 1101 A 1 
HETATM 10 N N19 GAR . . . B 2 -30.805 16.201 16.019 0.76 14.88 ? N19 GAR 1101 A 1 
HETATM 11 C C21 GAR . . . B 2 -29.726 15.529 15.604 0.76 17.89 ? C21 GAR 1101 A 1 
HETATM 12 O O22 GAR . . . B 2 -29.605 15.086 14.471 0.76 16 ? O22 GAR 1101 A 1 
HETATM 13 C C23 GAR . . . B 2 -28.609 15.34 16.597 0.76 21.93 ? C23 GAR 1101 A 1 
HETATM 14 N N24 GAR . . . B 2 -29.032 15.665 17.942 0.76 25.48 ? N24 GAR 1101 A 1 
HETATM 15 P P15 GAR . . . B 2 -35.91 20.822 14.89 0.76 12.76 ? P15 GAR 1101 A 1 
HETATM 16 O O16 GAR . . . B 2 -37.116 20.948 13.982 0.76 13.46 ? O16 GAR 1101 A 1 
HETATM 17 O O17 GAR . . . B 2 -34.932 21.984 14.826 0.76 13.85 ? O17 GAR 1101 A 1 
HETATM 18 O O18 GAR . . . B 2 -36.187 20.389 16.293 0.76 9.72 ? O18 GAR 1101 A 1 
#
_model_server_stats.io_time_ms              55 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           18 
#