data_8FDZ # _model_server_result.job_id v8_X-PNC5YhJ6lHkgYC1Ug _model_server_result.datetime_utc '2024-10-15 12:24:18' _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 8fdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1101}' # _entry.id 8FDZ # _exptl.entry_id 8FDZ _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 8FDZ _cell.length_a 74.879 _cell.length_b 74.879 _cell.length_c 100.616 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FDZ _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 83 n n C1 C2 GAR sing 84 n n C1 C5 GAR sing 85 n n C1 H1 GAR sing 86 n n O6 HO6 GAR sing 87 n n C2 O8 GAR sing 88 n n C2 C3 GAR sing 89 n n C2 H2 GAR sing 90 n n O8 HO8 GAR sing 91 n n C3 O4 GAR sing 92 n n C3 N19 GAR sing 93 n n C3 H3 GAR sing 94 n n O4 C5 GAR sing 95 n n C5 C10 GAR sing 96 n n C5 H5 GAR sing 97 n n C10 O12 GAR sing 98 n n C10 H101 GAR sing 99 n n C10 H102 GAR sing 100 n n O12 P15 GAR sing 101 n n N19 C21 GAR sing 102 n n N19 H19 GAR sing 103 n n C21 O22 GAR doub 104 n n C21 C23 GAR sing 105 n n C23 N24 GAR sing 106 n n C23 H231 GAR sing 107 n n C23 H232 GAR sing 108 n n N24 H241 GAR sing 109 n n N24 H242 GAR sing 110 n n P15 O16 GAR doub 111 n n P15 O17 GAR sing 112 n n P15 O18 GAR sing 113 n n # _atom_sites.entry_id 8FDZ _atom_sites.fract_transf_matrix[1][1] 0.013355 _atom_sites.fract_transf_matrix[1][2] 0.00771 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015421 _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] 0.009939 _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 1101 GAR GAR . C 3 XSO A 1 1102 1201 XSO F35 . D 4 HOH A 1 1201 46 HOH HOH . D 4 HOH A 2 1202 94 HOH HOH . D 4 HOH A 3 1203 2 HOH HOH . D 4 HOH A 4 1204 58 HOH HOH . D 4 HOH A 5 1205 13 HOH HOH . D 4 HOH A 6 1206 3 HOH HOH . D 4 HOH A 7 1207 35 HOH HOH . D 4 HOH A 8 1208 61 HOH HOH . D 4 HOH A 9 1209 31 HOH HOH . D 4 HOH A 10 1210 104 HOH HOH . D 4 HOH A 11 1211 20 HOH HOH . D 4 HOH A 12 1212 51 HOH HOH . D 4 HOH A 13 1213 7 HOH HOH . D 4 HOH A 14 1214 83 HOH HOH . D 4 HOH A 15 1215 106 HOH HOH . D 4 HOH A 16 1216 37 HOH HOH . D 4 HOH A 17 1217 71 HOH HOH . D 4 HOH A 18 1218 57 HOH HOH . D 4 HOH A 19 1219 50 HOH HOH . D 4 HOH A 20 1220 6 HOH HOH . D 4 HOH A 21 1221 26 HOH HOH . D 4 HOH A 22 1222 1 HOH HOH . D 4 HOH A 23 1223 67 HOH HOH . D 4 HOH A 24 1224 52 HOH HOH . D 4 HOH A 25 1225 30 HOH HOH . D 4 HOH A 26 1226 59 HOH HOH . D 4 HOH A 27 1227 11 HOH HOH . D 4 HOH A 28 1228 102 HOH HOH . D 4 HOH A 29 1229 17 HOH HOH . D 4 HOH A 30 1230 34 HOH HOH . D 4 HOH A 31 1231 40 HOH HOH . D 4 HOH A 32 1232 32 HOH HOH . D 4 HOH A 33 1233 99 HOH HOH . D 4 HOH A 34 1234 68 HOH HOH . D 4 HOH A 35 1235 4 HOH HOH . D 4 HOH A 36 1236 21 HOH HOH . D 4 HOH A 37 1237 14 HOH HOH . D 4 HOH A 38 1238 91 HOH HOH . D 4 HOH A 39 1239 74 HOH HOH . D 4 HOH A 40 1240 87 HOH HOH . D 4 HOH A 41 1241 22 HOH HOH . D 4 HOH A 42 1242 81 HOH HOH . D 4 HOH A 43 1243 16 HOH HOH . D 4 HOH A 44 1244 89 HOH HOH . D 4 HOH A 45 1245 42 HOH HOH . D 4 HOH A 46 1246 29 HOH HOH . D 4 HOH A 47 1247 5 HOH HOH . D 4 HOH A 48 1248 82 HOH HOH . D 4 HOH A 49 1249 66 HOH HOH . D 4 HOH A 50 1250 84 HOH HOH . D 4 HOH A 51 1251 36 HOH HOH . D 4 HOH A 52 1252 63 HOH HOH . D 4 HOH A 53 1253 25 HOH HOH . D 4 HOH A 54 1254 24 HOH HOH . D 4 HOH A 55 1255 100 HOH HOH . D 4 HOH A 56 1256 45 HOH HOH . D 4 HOH A 57 1257 15 HOH HOH . D 4 HOH A 58 1258 86 HOH HOH . D 4 HOH A 59 1259 27 HOH HOH . D 4 HOH A 60 1260 18 HOH HOH . D 4 HOH A 61 1261 8 HOH HOH . D 4 HOH A 62 1262 44 HOH HOH . D 4 HOH A 63 1263 39 HOH HOH . D 4 HOH A 64 1264 9 HOH HOH . D 4 HOH A 65 1265 64 HOH HOH . D 4 HOH A 66 1266 12 HOH HOH . D 4 HOH A 67 1267 48 HOH HOH . D 4 HOH A 68 1268 60 HOH HOH . D 4 HOH A 69 1269 96 HOH HOH . D 4 HOH A 70 1270 41 HOH HOH . D 4 HOH A 71 1271 98 HOH HOH . D 4 HOH A 72 1272 97 HOH HOH . D 4 HOH A 73 1273 55 HOH HOH . D 4 HOH A 74 1274 53 HOH HOH . D 4 HOH A 75 1275 43 HOH HOH . D 4 HOH A 76 1276 101 HOH HOH . D 4 HOH A 77 1277 95 HOH HOH . D 4 HOH A 78 1278 72 HOH HOH . D 4 HOH A 79 1279 33 HOH HOH . D 4 HOH A 80 1280 28 HOH HOH . D 4 HOH A 81 1281 69 HOH HOH . D 4 HOH A 82 1282 93 HOH HOH . D 4 HOH A 83 1283 105 HOH HOH . D 4 HOH A 84 1284 23 HOH HOH . D 4 HOH A 85 1285 73 HOH HOH . D 4 HOH A 86 1286 75 HOH HOH . D 4 HOH A 87 1287 10 HOH HOH . D 4 HOH A 88 1288 92 HOH HOH . D 4 HOH A 89 1289 62 HOH HOH . D 4 HOH A 90 1290 88 HOH HOH . D 4 HOH A 91 1291 54 HOH HOH . D 4 HOH A 92 1292 85 HOH HOH . D 4 HOH A 93 1293 70 HOH HOH . D 4 HOH A 94 1294 38 HOH HOH . D 4 HOH A 95 1295 103 HOH HOH . D 4 HOH A 96 1296 80 HOH HOH . D 4 HOH A 97 1297 76 HOH HOH . D 4 HOH A 98 1298 79 HOH HOH . D 4 HOH A 99 1299 47 HOH HOH . D 4 HOH A 100 1300 19 HOH HOH . D 4 HOH A 101 1301 90 HOH HOH . D 4 HOH A 102 1302 65 HOH HOH . D 4 HOH A 103 1303 77 HOH HOH . D 4 HOH A 104 1304 56 HOH HOH . D 4 HOH A 105 1305 78 HOH HOH . D 4 HOH A 106 1306 49 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 31.536 -21.082 -14.969 1 34.42 ? C1 GAR 1101 A 1 HETATM 2 O O6 GAR . . . B 2 30.978 -21.924 -13.964 1 36.69 ? O6 GAR 1101 A 1 HETATM 3 C C2 GAR . . . B 2 30.432 -20.507 -15.863 1 33.78 ? C2 GAR 1101 A 1 HETATM 4 O O8 GAR . . . B 2 29.341 -21.39 -16.002 1 35.87 ? O8 GAR 1101 A 1 HETATM 5 C C3 GAR . . . B 2 30.044 -19.221 -15.118 1 38.13 ? C3 GAR 1101 A 1 HETATM 6 O O4 GAR . . . B 2 31.247 -18.774 -14.46 1 40.3 ? O4 GAR 1101 A 1 HETATM 7 C C5 GAR . . . B 2 32.165 -19.867 -14.279 1 37.27 ? C5 GAR 1101 A 1 HETATM 8 C C10 GAR . . . B 2 33.529 -19.53 -14.837 1 39.82 ? C10 GAR 1101 A 1 HETATM 9 O O12 GAR . . . B 2 34.477 -20.446 -14.289 1 40.75 ? O12 GAR 1101 A 1 HETATM 10 N N19 GAR . . . B 2 29.513 -18.169 -15.938 1 42.78 ? N19 GAR 1101 A 1 HETATM 11 C C21 GAR . . . B 2 28.37 -17.564 -15.573 1 44.85 ? C21 GAR 1101 A 1 HETATM 12 O O22 GAR . . . B 2 27.784 -17.79 -14.505 1 38.41 ? O22 GAR 1101 A 1 HETATM 13 C C23 GAR . . . B 2 27.811 -16.552 -16.56 1 43.05 ? C23 GAR 1101 A 1 HETATM 14 N N24 GAR . . . B 2 26.651 -15.871 -16.008 1 43.05 ? N24 GAR 1101 A 1 HETATM 15 P P15 GAR . . . B 2 35.961 -20.491 -14.905 1 39.27 ? P15 GAR 1101 A 1 HETATM 16 O O16 GAR . . . B 2 35.78 -20.979 -16.329 1 36.81 ? O16 GAR 1101 A 1 HETATM 17 O O17 GAR . . . B 2 36.439 -19.051 -14.816 1 39.62 ? O17 GAR 1101 A 1 HETATM 18 O O18 GAR . . . B 2 36.675 -21.454 -13.972 1 40.4 ? O18 GAR 1101 A 1 HETATM 19 H H1 GAR . . . B 2 32.253 -21.676 -15.553 1 41.3 ? H1 GAR 1101 A 1 HETATM 20 H HO6 GAR . . . B 2 31.182 -22.847 -14.167 1 44.02 ? HO6 GAR 1101 A 1 HETATM 21 H H2 GAR . . . B 2 30.754 -20.336 -16.899 1 40.53 ? H2 GAR 1101 A 1 HETATM 22 H HO8 GAR . . . B 2 28.796 -21.113 -16.752 1 43.04 ? HO8 GAR 1101 A 1 HETATM 23 H H3 GAR . . . B 2 29.219 -19.462 -14.433 1 45.75 ? H3 GAR 1101 A 1 HETATM 24 H H5 GAR . . . B 2 32.326 -20.077 -13.212 1 44.73 ? H5 GAR 1101 A 1 HETATM 25 H H101 GAR . . . B 2 33.519 -19.606 -15.926 1 47.78 ? H101 GAR 1101 A 1 HETATM 26 H H102 GAR . . . B 2 33.801 -18.506 -14.574 1 47.78 ? H102 GAR 1101 A 1 HETATM 27 H H19 GAR . . . B 2 30.003 -17.896 -16.778 1 51.33 ? H19 GAR 1101 A 1 HETATM 28 H H231 GAR . . . B 2 27.528 -17.062 -17.483 1 51.65 ? H231 GAR 1101 A 1 HETATM 29 H H232 GAR . . . B 2 28.582 -15.818 -16.804 1 51.65 ? H232 GAR 1101 A 1 HETATM 30 H H241 GAR . . . B 2 26.325 -16.1 -15.081 1 51.66 ? H241 GAR 1101 A 1 HETATM 31 H H242 GAR . . . B 2 26.172 -15.168 -16.553 1 51.66 ? H242 GAR 1101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #