data_4NYI # _model_server_result.job_id '_fMOkEOK2GB1DL77sFhhBw' _model_server_result.datetime_utc '2024-11-23 01:03:14' _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 4nyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":202}' # _entry.id 4NYI # _exptl.entry_id 4NYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 90 _cell.entry_id 4NYI _cell.length_a 183.285 _cell.length_b 183.285 _cell.length_c 177.86 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 5 _struct_asym.id E _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 OG SER 18 Q SER 17 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc2 A OG1 THR 36 Q THR 35 1_555 D MG MG . Q MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc3 D MG MG . Q MG 201 1_555 E O1G GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc4 D MG MG . Q MG 201 1_555 E O1B GNP . Q GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 D MG MG . Q MG 201 1_555 G O HOH . Q HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 PG O1G GNP doub 196 n n PG O2G GNP sing 197 n n PG O3G GNP sing 198 n n PG N3B GNP sing 199 n n O2G HOG2 GNP sing 200 n n O3G HOG3 GNP sing 201 n n N3B PB GNP sing 202 n n N3B HNB3 GNP sing 203 n n PB O1B GNP doub 204 n n PB O2B GNP sing 205 n n PB O3A GNP sing 206 n n O2B HOB2 GNP sing 207 n n O3A PA GNP sing 208 n n PA O1A GNP doub 209 n n PA O2A GNP sing 210 n n PA O5' GNP sing 211 n n O2A HOA2 GNP sing 212 n n O5' C5' GNP sing 213 n n C5' C4' GNP sing 214 n n C5' "H5'2" GNP sing 215 n n C5' "H5'1" GNP sing 216 n n C4' O4' GNP sing 217 n n C4' C3' GNP sing 218 n n C4' H4' GNP sing 219 n n O4' C1' GNP sing 220 n n C3' O3' GNP sing 221 n n C3' C2' GNP sing 222 n n C3' H3' GNP sing 223 n n O3' HO3' GNP sing 224 n n C2' O2' GNP sing 225 n n C2' C1' GNP sing 226 n n C2' H2' GNP sing 227 n n O2' HO2' GNP sing 228 n n C1' N9 GNP sing 229 n n C1' H1' GNP sing 230 n n N9 C8 GNP sing 231 n y N9 C4 GNP sing 232 n y C8 N7 GNP doub 233 n y C8 H8 GNP sing 234 n n N7 C5 GNP sing 235 n y C5 C6 GNP sing 236 n y C5 C4 GNP doub 237 n y C6 O6 GNP doub 238 n n C6 N1 GNP sing 239 n y N1 C2 GNP sing 240 n y N1 HN1 GNP sing 241 n n C2 N2 GNP sing 242 n n C2 N3 GNP doub 243 n y N2 HN21 GNP sing 244 n n N2 HN22 GNP sing 245 n n N3 C4 GNP sing 246 n y # _atom_sites.entry_id 4NYI _atom_sites.fract_transf_matrix[1][1] 0.005456 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005456 _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] 0.005622 _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 4 MG Q 1 201 1002 MG MG . E 5 GNP Q 1 202 1001 GNP GNP . F 6 2PX S 1 1101 1 2PX LIG . G 7 HOH Q 1 301 1 HOH HOH . G 7 HOH Q 2 302 6 HOH HOH . G 7 HOH Q 3 303 13 HOH HOH . G 7 HOH Q 4 304 15 HOH HOH . G 7 HOH Q 5 305 23 HOH HOH . G 7 HOH Q 6 306 31 HOH HOH . G 7 HOH Q 7 307 33 HOH HOH . G 7 HOH Q 8 308 36 HOH HOH . G 7 HOH Q 9 309 50 HOH HOH . G 7 HOH Q 10 310 56 HOH HOH . G 7 HOH Q 11 311 58 HOH HOH . G 7 HOH Q 12 312 60 HOH HOH . G 7 HOH Q 13 313 63 HOH HOH . G 7 HOH Q 14 314 64 HOH HOH . G 7 HOH Q 15 315 66 HOH HOH . G 7 HOH Q 16 316 73 HOH HOH . G 7 HOH Q 17 317 94 HOH HOH . G 7 HOH Q 18 318 122 HOH HOH . G 7 HOH Q 19 319 123 HOH HOH . G 7 HOH Q 20 320 127 HOH HOH . G 7 HOH Q 21 321 134 HOH HOH . G 7 HOH Q 22 322 149 HOH HOH . G 7 HOH Q 23 323 151 HOH HOH . G 7 HOH Q 24 324 156 HOH HOH . H 7 HOH R 1 201 7 HOH HOH . H 7 HOH R 2 202 10 HOH HOH . H 7 HOH R 3 203 16 HOH HOH . H 7 HOH R 4 204 17 HOH HOH . H 7 HOH R 5 205 21 HOH HOH . H 7 HOH R 6 206 38 HOH HOH . H 7 HOH R 7 207 40 HOH HOH . H 7 HOH R 8 208 41 HOH HOH . H 7 HOH R 9 209 43 HOH HOH . H 7 HOH R 10 210 47 HOH HOH . H 7 HOH R 11 211 49 HOH HOH . H 7 HOH R 12 212 52 HOH HOH . H 7 HOH R 13 213 54 HOH HOH . H 7 HOH R 14 214 59 HOH HOH . H 7 HOH R 15 215 68 HOH HOH . H 7 HOH R 16 216 70 HOH HOH . H 7 HOH R 17 217 71 HOH HOH . H 7 HOH R 18 218 72 HOH HOH . H 7 HOH R 19 219 92 HOH HOH . H 7 HOH R 20 220 93 HOH HOH . H 7 HOH R 21 221 95 HOH HOH . H 7 HOH R 22 222 114 HOH HOH . H 7 HOH R 23 223 115 HOH HOH . H 7 HOH R 24 224 125 HOH HOH . H 7 HOH R 25 225 132 HOH HOH . H 7 HOH R 26 226 140 HOH HOH . H 7 HOH R 27 227 143 HOH HOH . H 7 HOH R 28 228 147 HOH HOH . H 7 HOH R 29 229 155 HOH HOH . I 7 HOH S 1 1201 2 HOH HOH . I 7 HOH S 2 1202 4 HOH HOH . I 7 HOH S 3 1203 5 HOH HOH . I 7 HOH S 4 1204 8 HOH HOH . I 7 HOH S 5 1205 9 HOH HOH . I 7 HOH S 6 1206 11 HOH HOH . I 7 HOH S 7 1207 12 HOH HOH . I 7 HOH S 8 1208 14 HOH HOH . I 7 HOH S 9 1209 18 HOH HOH . I 7 HOH S 10 1210 19 HOH HOH . I 7 HOH S 11 1211 20 HOH HOH . I 7 HOH S 12 1212 22 HOH HOH . I 7 HOH S 13 1213 24 HOH HOH . I 7 HOH S 14 1214 25 HOH HOH . I 7 HOH S 15 1215 26 HOH HOH . I 7 HOH S 16 1216 27 HOH HOH . I 7 HOH S 17 1217 29 HOH HOH . I 7 HOH S 18 1218 30 HOH HOH . I 7 HOH S 19 1219 34 HOH HOH . I 7 HOH S 20 1220 35 HOH HOH . I 7 HOH S 21 1221 37 HOH HOH . I 7 HOH S 22 1222 44 HOH HOH . I 7 HOH S 23 1223 45 HOH HOH . I 7 HOH S 24 1224 46 HOH HOH . I 7 HOH S 25 1225 48 HOH HOH . I 7 HOH S 26 1226 51 HOH HOH . I 7 HOH S 27 1227 53 HOH HOH . I 7 HOH S 28 1228 55 HOH HOH . I 7 HOH S 29 1229 57 HOH HOH . I 7 HOH S 30 1230 61 HOH HOH . I 7 HOH S 31 1231 62 HOH HOH . I 7 HOH S 32 1232 65 HOH HOH . I 7 HOH S 33 1233 67 HOH HOH . I 7 HOH S 34 1234 69 HOH HOH . I 7 HOH S 35 1235 75 HOH HOH . I 7 HOH S 36 1236 76 HOH HOH . I 7 HOH S 37 1237 77 HOH HOH . I 7 HOH S 38 1238 78 HOH HOH . I 7 HOH S 39 1239 79 HOH HOH . I 7 HOH S 40 1240 80 HOH HOH . I 7 HOH S 41 1241 81 HOH HOH . I 7 HOH S 42 1242 82 HOH HOH . I 7 HOH S 43 1243 83 HOH HOH . I 7 HOH S 44 1244 84 HOH HOH . I 7 HOH S 45 1245 85 HOH HOH . I 7 HOH S 46 1246 86 HOH HOH . I 7 HOH S 47 1247 87 HOH HOH . I 7 HOH S 48 1248 88 HOH HOH . I 7 HOH S 49 1249 89 HOH HOH . I 7 HOH S 50 1250 90 HOH HOH . I 7 HOH S 51 1251 91 HOH HOH . I 7 HOH S 52 1252 96 HOH HOH . I 7 HOH S 53 1253 97 HOH HOH . I 7 HOH S 54 1254 98 HOH HOH . I 7 HOH S 55 1255 99 HOH HOH . I 7 HOH S 56 1256 100 HOH HOH . I 7 HOH S 57 1257 101 HOH HOH . I 7 HOH S 58 1258 102 HOH HOH . I 7 HOH S 59 1259 103 HOH HOH . I 7 HOH S 60 1260 104 HOH HOH . I 7 HOH S 61 1261 105 HOH HOH . I 7 HOH S 62 1262 106 HOH HOH . I 7 HOH S 63 1263 107 HOH HOH . I 7 HOH S 64 1264 108 HOH HOH . I 7 HOH S 65 1265 109 HOH HOH . I 7 HOH S 66 1266 110 HOH HOH . I 7 HOH S 67 1267 112 HOH HOH . I 7 HOH S 68 1268 113 HOH HOH . I 7 HOH S 69 1269 116 HOH HOH . I 7 HOH S 70 1270 117 HOH HOH . I 7 HOH S 71 1271 119 HOH HOH . I 7 HOH S 72 1272 121 HOH HOH . I 7 HOH S 73 1273 124 HOH HOH . I 7 HOH S 74 1274 126 HOH HOH . I 7 HOH S 75 1275 128 HOH HOH . I 7 HOH S 76 1276 130 HOH HOH . I 7 HOH S 77 1277 131 HOH HOH . I 7 HOH S 78 1278 133 HOH HOH . I 7 HOH S 79 1279 135 HOH HOH . I 7 HOH S 80 1280 138 HOH HOH . I 7 HOH S 81 1281 139 HOH HOH . I 7 HOH S 82 1282 141 HOH HOH . I 7 HOH S 83 1283 142 HOH HOH . I 7 HOH S 84 1284 144 HOH HOH . I 7 HOH S 85 1285 145 HOH HOH . I 7 HOH S 86 1286 146 HOH HOH . I 7 HOH S 87 1287 148 HOH HOH . I 7 HOH S 88 1288 150 HOH HOH . I 7 HOH S 89 1289 152 HOH HOH . I 7 HOH S 90 1290 153 HOH HOH . I 7 HOH S 91 1291 154 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 P PG GNP . . . E 5 14.094 51.463 69.995 1 28.49 ? PG GNP 202 Q 1 HETATM 2 O O1G GNP . . . E 5 14.269 50.249 69.103 1 25.57 ? O1G GNP 202 Q 1 HETATM 3 O O2G GNP . . . E 5 12.908 51.327 70.922 1 22.49 ? O2G GNP 202 Q 1 HETATM 4 O O3G GNP . . . E 5 15.258 51.802 70.906 1 14.99 ? O3G GNP 202 Q 1 HETATM 5 N N3B GNP . . . E 5 13.861 52.718 69.008 1 25.63 ? N3B GNP 202 Q 1 HETATM 6 P PB GNP . . . E 5 14.804 53.265 67.819 1 19.62 ? PB GNP 202 Q 1 HETATM 7 O O1B GNP . . . E 5 15.254 52.106 67.003 1 15.79 ? O1B GNP 202 Q 1 HETATM 8 O O2B GNP . . . E 5 15.874 54.115 68.382 1 19.94 ? O2B GNP 202 Q 1 HETATM 9 O O3A GNP . . . E 5 13.964 54.204 66.938 1 18.68 ? O3A GNP 202 Q 1 HETATM 10 P PA GNP . . . E 5 13.314 53.823 65.596 1 19.2 ? PA GNP 202 Q 1 HETATM 11 O O1A GNP . . . E 5 14.4 53.622 64.62 1 21.09 ? O1A GNP 202 Q 1 HETATM 12 O O2A GNP . . . E 5 12.34 52.721 65.743 1 18.92 ? O2A GNP 202 Q 1 HETATM 13 O O5' GNP . . . E 5 12.482 55.056 65.071 1 17.86 ? O5' GNP 202 Q 1 HETATM 14 C C5' GNP . . . E 5 11.639 55.749 65.975 1 20.08 ? C5' GNP 202 Q 1 HETATM 15 C C4' GNP . . . E 5 10.593 56.591 65.262 1 22.75 ? C4' GNP 202 Q 1 HETATM 16 O O4' GNP . . . E 5 11.166 57.832 64.778 1 19.42 ? O4' GNP 202 Q 1 HETATM 17 C C3' GNP . . . E 5 9.909 55.969 64.061 1 24.73 ? C3' GNP 202 Q 1 HETATM 18 O O3' GNP . . . E 5 8.562 56.438 64.055 1 28.27 ? O3' GNP 202 Q 1 HETATM 19 C C2' GNP . . . E 5 10.759 56.497 62.905 1 21.57 ? C2' GNP 202 Q 1 HETATM 20 O O2' GNP . . . E 5 10.061 56.562 61.673 1 28.47 ? O2' GNP 202 Q 1 HETATM 21 C C1' GNP . . . E 5 11.128 57.899 63.383 1 20.21 ? C1' GNP 202 Q 1 HETATM 22 N N9 GNP . . . E 5 12.436 58.342 62.911 1 22.82 ? N9 GNP 202 Q 1 HETATM 23 C C8 GNP . . . E 5 13.632 57.679 63.066 1 24.19 ? C8 GNP 202 Q 1 HETATM 24 N N7 GNP . . . E 5 14.648 58.304 62.534 1 24.08 ? N7 GNP 202 Q 1 HETATM 25 C C5 GNP . . . E 5 14.091 59.452 61.978 1 22.45 ? C5 GNP 202 Q 1 HETATM 26 C C6 GNP . . . E 5 14.702 60.512 61.261 1 22.3 ? C6 GNP 202 Q 1 HETATM 27 O O6 GNP . . . E 5 15.894 60.654 60.967 1 20.4 ? O6 GNP 202 Q 1 HETATM 28 N N1 GNP . . . E 5 13.783 61.487 60.875 1 30.49 ? N1 GNP 202 Q 1 HETATM 29 C C2 GNP . . . E 5 12.435 61.443 61.148 1 30.04 ? C2 GNP 202 Q 1 HETATM 30 N N2 GNP . . . E 5 11.713 62.479 60.7 1 25.94 ? N2 GNP 202 Q 1 HETATM 31 N N3 GNP . . . E 5 11.847 60.454 61.819 1 28.45 ? N3 GNP 202 Q 1 HETATM 32 C C4 GNP . . . E 5 12.73 59.493 62.205 1 24.07 ? C4 GNP 202 Q 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #