data_1PR5 # _model_server_result.job_id 5PGL5mauJi_-WtNPU2_pFw _model_server_result.datetime_utc '2024-11-04 23:45:56' _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 1pr5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1245}' # _entry.id 1PR5 # _exptl.entry_id 1PR5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 266.253 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "'2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL" _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 1PR5 _cell.length_a 120.8 _cell.length_b 120.8 _cell.length_c 239.9 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PR5 _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 39.983333 # 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 'C11 H14 N4 O4' _chem_comp.formula_weight 266.253 _chem_comp.id TBN _chem_comp.mon_nstd_flag n _chem_comp.name "'2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 7-DEAZAADENOSINE # 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' TBN sing 294 n n O5' H5' TBN sing 295 n n C5' C4' TBN sing 296 n n C5' "H5'1" TBN sing 297 n n C5' "H5'2" TBN sing 298 n n C4' O4' TBN sing 299 n n C4' C3' TBN sing 300 n n C4' H4' TBN sing 301 n n O4' C1' TBN sing 302 n n C1' N9 TBN sing 303 n n C1' C2' TBN sing 304 n n C1' H1' TBN sing 305 n n N9 C8 TBN sing 306 n y N9 C4 TBN sing 307 n y C8 C7 TBN doub 308 n y C8 H8 TBN sing 309 n n C7 C5 TBN sing 310 n y C7 H7 TBN sing 311 n n C5 C6 TBN doub 312 n y C5 C4 TBN sing 313 n y C6 N1 TBN sing 314 n y C6 N6 TBN sing 315 n n N1 C2 TBN doub 316 n y C2 N3 TBN sing 317 n y C2 H2 TBN sing 318 n n N3 C4 TBN doub 319 n y N6 HN61 TBN sing 320 n n N6 HN62 TBN sing 321 n n C2' O2' TBN sing 322 n n C2' C3' TBN sing 323 n n C2' H2' TBN sing 324 n n O2' H1 TBN sing 325 n n C3' O3' TBN sing 326 n n C3' H3' TBN sing 327 n n O3' H3 TBN sing 328 n n # _atom_sites.entry_id 1PR5 _atom_sites.fract_transf_matrix[1][1] 0.008278 _atom_sites.fract_transf_matrix[1][2] 0.004779 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009559 _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] 0.004168 _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 TBN A 1 1245 245 TBN TBN . F 2 PO4 B 1 1249 247 PO4 PO4 . G 3 TBN B 1 1246 245 TBN TBN . H 2 PO4 C 1 1250 247 PO4 PO4 . I 3 TBN C 1 1247 245 TBN TBN . J 4 HOH A 1 1249 1 HOH WAT . J 4 HOH A 2 1250 2 HOH WAT . J 4 HOH A 3 1251 3 HOH WAT . J 4 HOH A 4 1252 4 HOH WAT . J 4 HOH A 5 1253 5 HOH WAT . J 4 HOH A 6 1254 7 HOH WAT . J 4 HOH A 7 1255 8 HOH WAT . J 4 HOH A 8 1256 9 HOH WAT . J 4 HOH A 9 1257 10 HOH WAT . J 4 HOH A 10 1258 11 HOH WAT . J 4 HOH A 11 1259 12 HOH WAT . J 4 HOH A 12 1260 13 HOH WAT . J 4 HOH A 13 1261 15 HOH WAT . J 4 HOH A 14 1262 16 HOH WAT . J 4 HOH A 15 1263 17 HOH WAT . J 4 HOH A 16 1264 18 HOH WAT . J 4 HOH A 17 1265 19 HOH WAT . J 4 HOH A 18 1266 20 HOH WAT . J 4 HOH A 19 1267 21 HOH WAT . J 4 HOH A 20 1268 22 HOH WAT . J 4 HOH A 21 1269 23 HOH WAT . J 4 HOH A 22 1270 24 HOH WAT . J 4 HOH A 23 1271 25 HOH WAT . J 4 HOH A 24 1272 26 HOH WAT . J 4 HOH A 25 1273 27 HOH WAT . J 4 HOH A 26 1274 28 HOH WAT . J 4 HOH A 27 1275 30 HOH WAT . J 4 HOH A 28 1276 31 HOH WAT . J 4 HOH A 29 1277 32 HOH WAT . J 4 HOH A 30 1278 33 HOH WAT . J 4 HOH A 31 1279 35 HOH WAT . J 4 HOH A 32 1280 36 HOH WAT . J 4 HOH A 33 1281 37 HOH WAT . J 4 HOH A 34 1282 38 HOH WAT . J 4 HOH A 35 1283 40 HOH WAT . J 4 HOH A 36 1284 42 HOH WAT . J 4 HOH A 37 1285 43 HOH WAT . J 4 HOH A 38 1286 44 HOH WAT . J 4 HOH A 39 1287 45 HOH WAT . J 4 HOH A 40 1288 46 HOH WAT . J 4 HOH A 41 1289 47 HOH WAT . J 4 HOH A 42 1290 48 HOH WAT . J 4 HOH A 43 1291 104 HOH WAT . J 4 HOH A 44 1292 105 HOH WAT . K 4 HOH B 1 1250 29 HOH WAT . K 4 HOH B 2 1251 39 HOH WAT . K 4 HOH B 3 1252 41 HOH WAT . K 4 HOH B 4 1253 49 HOH WAT . K 4 HOH B 5 1254 50 HOH WAT . K 4 HOH B 6 1255 51 HOH WAT . K 4 HOH B 7 1256 52 HOH WAT . K 4 HOH B 8 1257 53 HOH WAT . K 4 HOH B 9 1258 54 HOH WAT . K 4 HOH B 10 1259 55 HOH WAT . K 4 HOH B 11 1260 56 HOH WAT . K 4 HOH B 12 1261 57 HOH WAT . K 4 HOH B 13 1262 58 HOH WAT . K 4 HOH B 14 1263 59 HOH WAT . K 4 HOH B 15 1264 60 HOH WAT . K 4 HOH B 16 1265 61 HOH WAT . K 4 HOH B 17 1266 62 HOH WAT . K 4 HOH B 18 1267 63 HOH WAT . K 4 HOH B 19 1268 64 HOH WAT . K 4 HOH B 20 1269 66 HOH WAT . K 4 HOH B 21 1270 67 HOH WAT . K 4 HOH B 22 1271 68 HOH WAT . K 4 HOH B 23 1272 69 HOH WAT . K 4 HOH B 24 1273 70 HOH WAT . K 4 HOH B 25 1274 71 HOH WAT . K 4 HOH B 26 1275 72 HOH WAT . K 4 HOH B 27 1276 73 HOH WAT . K 4 HOH B 28 1277 74 HOH WAT . K 4 HOH B 29 1278 75 HOH WAT . K 4 HOH B 30 1279 76 HOH WAT . K 4 HOH B 31 1280 77 HOH WAT . K 4 HOH B 32 1281 78 HOH WAT . K 4 HOH B 33 1282 79 HOH WAT . K 4 HOH B 34 1283 80 HOH WAT . K 4 HOH B 35 1284 81 HOH WAT . K 4 HOH B 36 1285 82 HOH WAT . K 4 HOH B 37 1286 83 HOH WAT . K 4 HOH B 38 1287 84 HOH WAT . K 4 HOH B 39 1288 106 HOH WAT . L 4 HOH C 1 1251 14 HOH WAT . L 4 HOH C 2 1252 34 HOH WAT . L 4 HOH C 3 1253 65 HOH WAT . L 4 HOH C 4 1254 85 HOH WAT . L 4 HOH C 5 1255 86 HOH WAT . L 4 HOH C 6 1256 87 HOH WAT . L 4 HOH C 7 1257 88 HOH WAT . L 4 HOH C 8 1258 89 HOH WAT . L 4 HOH C 9 1259 90 HOH WAT . L 4 HOH C 10 1260 91 HOH WAT . L 4 HOH C 11 1261 92 HOH WAT . L 4 HOH C 12 1262 93 HOH WAT . L 4 HOH C 13 1263 94 HOH WAT . L 4 HOH C 14 1264 95 HOH WAT . L 4 HOH C 15 1265 96 HOH WAT . L 4 HOH C 16 1266 97 HOH WAT . L 4 HOH C 17 1267 98 HOH WAT . L 4 HOH C 18 1268 99 HOH WAT . L 4 HOH C 19 1269 100 HOH WAT . L 4 HOH C 20 1270 101 HOH WAT . L 4 HOH C 21 1271 102 HOH WAT . L 4 HOH C 22 1272 103 HOH WAT . L 4 HOH C 23 1273 108 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' TBN . . . E 3 93.102 65.343 17.035 1 51.63 ? O5' TBN 1245 A 1 HETATM 2 C C5' TBN . . . E 3 92.952 64.241 17.949 1 51.35 ? C5' TBN 1245 A 1 HETATM 3 C C4' TBN . . . E 3 93.363 64.633 19.391 1 51.21 ? C4' TBN 1245 A 1 HETATM 4 O O4' TBN . . . E 3 93.051 65.998 19.698 1 51.46 ? O4' TBN 1245 A 1 HETATM 5 C C1' TBN . . . E 3 91.875 66.056 20.521 1 50.96 ? C1' TBN 1245 A 1 HETATM 6 N N9 TBN . . . E 3 90.832 66.775 19.722 1 50.17 ? N9 TBN 1245 A 1 HETATM 7 C C8 TBN . . . E 3 90.728 68.158 19.565 1 49.76 ? C8 TBN 1245 A 1 HETATM 8 C C7 TBN . . . E 3 89.667 68.478 18.767 1 50.28 ? C7 TBN 1245 A 1 HETATM 9 C C5 TBN . . . E 3 89.092 67.296 18.413 1 51.34 ? C5 TBN 1245 A 1 HETATM 10 C C6 TBN . . . E 3 87.954 67.112 17.581 1 51.99 ? C6 TBN 1245 A 1 HETATM 11 N N1 TBN . . . E 3 87.6 65.79 17.398 1 51.33 ? N1 TBN 1245 A 1 HETATM 12 C C2 TBN . . . E 3 88.319 64.797 17.991 1 50.78 ? C2 TBN 1245 A 1 HETATM 13 N N3 TBN . . . E 3 89.413 64.904 18.792 1 50.97 ? N3 TBN 1245 A 1 HETATM 14 C C4 TBN . . . E 3 89.764 66.227 18.972 1 50.61 ? C4 TBN 1245 A 1 HETATM 15 N N6 TBN . . . E 3 87.263 68.11 17.006 1 52.37 ? N6 TBN 1245 A 1 HETATM 16 C C2' TBN . . . E 3 91.616 64.647 21.089 1 50.51 ? C2' TBN 1245 A 1 HETATM 17 O O2' TBN . . . E 3 91.814 64.719 22.502 1 50.1 ? O2' TBN 1245 A 1 HETATM 18 C C3' TBN . . . E 3 92.629 63.741 20.397 1 50.75 ? C3' TBN 1245 A 1 HETATM 19 O O3' TBN . . . E 3 93.502 63.055 21.31 1 51.84 ? O3' TBN 1245 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #