data_8EM0 # _model_server_result.job_id il3oIiJnKNnIYy00v1bo3Q _model_server_result.datetime_utc '2025-02-16 12:09:27' _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 8em0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8EM0 # _exptl.entry_id 8EM0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _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 120 _cell.entry_id 8EM0 _cell.length_a 89.146 _cell.length_b 89.146 _cell.length_c 135.545 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EM0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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,E,F _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 # 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 17 A SER 17 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc2 A O PHE 28 A PHE 28 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc3 A OD1 ASP 30 A ASP 30 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc4 A OE1 GLU 31 A GLU 31 1_555 C CA CA . A CA 202 5_674 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc5 A OD1 ASP 33 A ASP 33 1_555 C CA CA . A CA 202 5_674 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc6 A OD2 ASP 33 A ASP 33 1_555 C CA CA . A CA 202 5_674 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc7 A OG1 THR 35 A THR 35 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc8 B O2G GNP . A GNP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc9 B O2B GNP . A GNP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc10 C CA CA . A CA 202 1_555 F O HOH . A HOH 338 5_674 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc11 C CA CA . A CA 202 1_555 F O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc12 D MG MG . A MG 203 1_555 F O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc13 D MG MG . A MG 203 1_555 F O HOH . A HOH 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc14 E MG MG . A MG 204 1_555 F O HOH . A HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc15 E MG MG . A MG 204 1_555 F O HOH . A HOH 317 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc16 E MG MG . A MG 204 1_555 F O HOH . A HOH 388 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc17 E MG MG . A MG 204 1_555 F O HOH . A HOH 388 3_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? # _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 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 8EM0 _atom_sites.fract_transf_matrix[1][1] 0.011218 _atom_sites.fract_transf_matrix[1][2] 0.006476 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012953 _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] 0.007378 _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 GNP A 1 201 167 GNP GNP . C 3 CA A 1 202 168 CA CA . D 4 MG A 1 203 169 MG MG . E 4 MG A 1 204 170 MG MG . F 5 HOH A 1 301 272 HOH HOH . F 5 HOH A 2 302 227 HOH HOH . F 5 HOH A 3 303 281 HOH HOH . F 5 HOH A 4 304 264 HOH HOH . F 5 HOH A 5 305 211 HOH HOH . F 5 HOH A 6 306 256 HOH HOH . F 5 HOH A 7 307 302 HOH HOH . F 5 HOH A 8 308 261 HOH HOH . F 5 HOH A 9 309 186 HOH HOH . F 5 HOH A 10 310 212 HOH HOH . F 5 HOH A 11 311 244 HOH HOH . F 5 HOH A 12 312 305 HOH HOH . F 5 HOH A 13 313 253 HOH HOH . F 5 HOH A 14 314 228 HOH HOH . F 5 HOH A 15 315 284 HOH HOH . F 5 HOH A 16 316 215 HOH HOH . F 5 HOH A 17 317 185 HOH HOH . F 5 HOH A 18 318 184 HOH HOH . F 5 HOH A 19 319 301 HOH HOH . F 5 HOH A 20 320 181 HOH HOH . F 5 HOH A 21 321 218 HOH HOH . F 5 HOH A 22 322 263 HOH HOH . F 5 HOH A 23 323 266 HOH HOH . F 5 HOH A 24 324 230 HOH HOH . F 5 HOH A 25 325 205 HOH HOH . F 5 HOH A 26 326 176 HOH HOH . F 5 HOH A 27 327 238 HOH HOH . F 5 HOH A 28 328 209 HOH HOH . F 5 HOH A 29 329 206 HOH HOH . F 5 HOH A 30 330 248 HOH HOH . F 5 HOH A 31 331 225 HOH HOH . F 5 HOH A 32 332 172 HOH HOH . F 5 HOH A 33 333 294 HOH HOH . F 5 HOH A 34 334 249 HOH HOH . F 5 HOH A 35 335 280 HOH HOH . F 5 HOH A 36 336 174 HOH HOH . F 5 HOH A 37 337 222 HOH HOH . F 5 HOH A 38 338 200 HOH HOH . F 5 HOH A 39 339 189 HOH HOH . F 5 HOH A 40 340 254 HOH HOH . F 5 HOH A 41 341 198 HOH HOH . F 5 HOH A 42 342 262 HOH HOH . F 5 HOH A 43 343 233 HOH HOH . F 5 HOH A 44 344 197 HOH HOH . F 5 HOH A 45 345 175 HOH HOH . F 5 HOH A 46 346 196 HOH HOH . F 5 HOH A 47 347 194 HOH HOH . F 5 HOH A 48 348 193 HOH HOH . F 5 HOH A 49 349 219 HOH HOH . F 5 HOH A 50 350 203 HOH HOH . F 5 HOH A 51 351 183 HOH HOH . F 5 HOH A 52 352 191 HOH HOH . F 5 HOH A 53 353 171 HOH HOH . F 5 HOH A 54 354 291 HOH HOH . F 5 HOH A 55 355 288 HOH HOH . F 5 HOH A 56 356 290 HOH HOH . F 5 HOH A 57 357 178 HOH HOH . F 5 HOH A 58 358 229 HOH HOH . F 5 HOH A 59 359 236 HOH HOH . F 5 HOH A 60 360 293 HOH HOH . F 5 HOH A 61 361 298 HOH HOH . F 5 HOH A 62 362 207 HOH HOH . F 5 HOH A 63 363 173 HOH HOH . F 5 HOH A 64 364 240 HOH HOH . F 5 HOH A 65 365 187 HOH HOH . F 5 HOH A 66 366 202 HOH HOH . F 5 HOH A 67 367 241 HOH HOH . F 5 HOH A 68 368 257 HOH HOH . F 5 HOH A 69 369 208 HOH HOH . F 5 HOH A 70 370 216 HOH HOH . F 5 HOH A 71 371 271 HOH HOH . F 5 HOH A 72 372 199 HOH HOH . F 5 HOH A 73 373 224 HOH HOH . F 5 HOH A 74 374 296 HOH HOH . F 5 HOH A 75 375 259 HOH HOH . F 5 HOH A 76 376 226 HOH HOH . F 5 HOH A 77 377 221 HOH HOH . F 5 HOH A 78 378 237 HOH HOH . F 5 HOH A 79 379 242 HOH HOH . F 5 HOH A 80 380 295 HOH HOH . F 5 HOH A 81 381 232 HOH HOH . F 5 HOH A 82 382 201 HOH HOH . F 5 HOH A 83 383 289 HOH HOH . F 5 HOH A 84 384 177 HOH HOH . F 5 HOH A 85 385 223 HOH HOH . F 5 HOH A 86 386 297 HOH HOH . F 5 HOH A 87 387 204 HOH HOH . F 5 HOH A 88 388 182 HOH HOH . F 5 HOH A 89 389 275 HOH HOH . F 5 HOH A 90 390 217 HOH HOH . F 5 HOH A 91 391 179 HOH HOH . F 5 HOH A 92 392 213 HOH HOH . F 5 HOH A 93 393 267 HOH HOH . F 5 HOH A 94 394 265 HOH HOH . F 5 HOH A 95 395 274 HOH HOH . F 5 HOH A 96 396 285 HOH HOH . F 5 HOH A 97 397 278 HOH HOH . F 5 HOH A 98 398 287 HOH HOH . F 5 HOH A 99 399 292 HOH HOH . F 5 HOH A 100 400 245 HOH HOH . F 5 HOH A 101 401 195 HOH HOH . F 5 HOH A 102 402 210 HOH HOH . F 5 HOH A 103 403 268 HOH HOH . F 5 HOH A 104 404 300 HOH HOH . F 5 HOH A 105 405 243 HOH HOH . F 5 HOH A 106 406 247 HOH HOH . F 5 HOH A 107 407 192 HOH HOH . F 5 HOH A 108 408 252 HOH HOH . F 5 HOH A 109 409 258 HOH HOH . F 5 HOH A 110 410 306 HOH HOH . F 5 HOH A 111 411 190 HOH HOH . F 5 HOH A 112 412 286 HOH HOH . F 5 HOH A 113 413 276 HOH HOH . F 5 HOH A 114 414 180 HOH HOH . F 5 HOH A 115 415 282 HOH HOH . F 5 HOH A 116 416 273 HOH HOH . F 5 HOH A 117 417 250 HOH HOH . F 5 HOH A 118 418 303 HOH HOH . F 5 HOH A 119 419 231 HOH HOH . F 5 HOH A 120 420 277 HOH HOH . F 5 HOH A 121 421 234 HOH HOH . F 5 HOH A 122 422 239 HOH HOH . F 5 HOH A 123 423 283 HOH HOH . F 5 HOH A 124 424 304 HOH HOH . F 5 HOH A 125 425 270 HOH HOH . F 5 HOH A 126 426 246 HOH HOH . F 5 HOH A 127 427 214 HOH HOH . F 5 HOH A 128 428 279 HOH HOH . F 5 HOH A 129 429 269 HOH HOH . F 5 HOH A 130 430 188 HOH HOH . F 5 HOH A 131 431 235 HOH HOH . F 5 HOH A 132 432 255 HOH HOH . F 5 HOH A 133 433 220 HOH HOH . F 5 HOH A 134 434 299 HOH HOH . F 5 HOH A 135 435 251 HOH HOH . F 5 HOH A 136 436 307 HOH HOH . F 5 HOH A 137 437 260 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 . . . B 2 -9.65 65.065 -67.866 1 23.21 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . B 2 -8.774 64.64 -66.7 1 22.31 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . B 2 -10.638 66.156 -67.502 1 26.93 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . B 2 -10.315 63.796 -68.352 1 23.59 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . B 2 -8.73 65.62 -69.083 1 22.32 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . B 2 -9.218 66.271 -70.479 1 22.48 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . B 2 -9.669 65.237 -71.445 1 18.64 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . B 2 -10.241 67.305 -70.181 1 18.93 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . B 2 -8.022 66.964 -71.169 1 21.99 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . B 2 -7.733 68.482 -71.109 1 24.16 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . B 2 -8.676 69.225 -71.983 1 22.72 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . B 2 -7.626 68.969 -69.707 1 18.89 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . B 2 -6.307 68.683 -71.761 1 24.2 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . B 2 -5.186 67.862 -71.411 1 24.37 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . B 2 -3.895 68.511 -71.885 1 20.87 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . B 2 -3.784 68.35 -73.329 1 22.06 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . B 2 -3.814 70.017 -71.631 1 26.89 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . B 2 -2.471 70.404 -71.334 1 21.12 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . B 2 -4.262 70.622 -72.964 1 22.86 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . B 2 -3.688 71.887 -73.215 1 21.54 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . B 2 -3.727 69.605 -73.969 1 20.75 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . B 2 -4.569 69.563 -75.159 1 25.96 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . B 2 -5.926 69.362 -75.208 1 21.79 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . B 2 -6.404 69.392 -76.421 1 25.51 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . B 2 -5.305 69.628 -77.234 1 20.63 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . B 2 -5.205 69.757 -78.65 1 25.73 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . B 2 -6.1 69.697 -79.527 1 24.11 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . B 2 -3.886 69.997 -79.035 1 25.5 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . B 2 -2.815 70.085 -78.171 1 27.84 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . B 2 -1.616 70.31 -78.725 1 27.13 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . B 2 -2.902 69.96 -76.856 1 25.43 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . B 2 -4.172 69.737 -76.461 1 22.36 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #