data_4XVQ # _model_server_result.job_id 3_I96Rd4BrvvvWR2iyu8JQ _model_server_result.datetime_utc '2024-12-09 01:18:44' _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 4xvq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4XVQ # _exptl.entry_id 4XVQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _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 4XVQ _cell.length_a 39.046 _cell.length_b 39.046 _cell.length_c 158.737 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XVQ _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,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 3 _struct_asym.id C _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 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc2 A O ASN 26 A ASN 26 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc3 A OG1 THR 35 A THR 35 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc4 A OD2 ASP 107 A ASP 107 1_555 D MG MG . A MG 203 1_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc5 B MG MG . A MG 201 1_555 C O1G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc6 B MG MG . A MG 201 1_555 C O1B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc7 B MG MG . A MG 201 1_555 F O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc8 B MG MG . A MG 201 1_555 F O HOH . A HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc9 D MG MG . A MG 203 1_555 F O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc10 D MG MG . A MG 203 1_555 F O HOH . A HOH 348 1_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? # _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 4XVQ _atom_sites.fract_transf_matrix[1][1] 0.025611 _atom_sites.fract_transf_matrix[1][2] 0.014786 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.029573 _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] 0.0063 _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 MG A 1 201 529 MG MG . C 3 GNP A 1 202 528 GNP GNP . D 2 MG A 1 203 530 MG MG . E 4 GOL A 1 204 1000 GOL GOL . F 5 HOH A 1 301 274 HOH HOH . F 5 HOH A 2 302 268 HOH HOH . F 5 HOH A 3 303 267 HOH HOH . F 5 HOH A 4 304 297 HOH HOH . F 5 HOH A 5 305 296 HOH HOH . F 5 HOH A 6 306 215 HOH HOH . F 5 HOH A 7 307 273 HOH HOH . F 5 HOH A 8 308 295 HOH HOH . F 5 HOH A 9 309 230 HOH HOH . F 5 HOH A 10 310 208 HOH HOH . F 5 HOH A 11 311 243 HOH HOH . F 5 HOH A 12 312 242 HOH HOH . F 5 HOH A 13 313 218 HOH HOH . F 5 HOH A 14 314 272 HOH HOH . F 5 HOH A 15 315 217 HOH HOH . F 5 HOH A 16 316 203 HOH HOH . F 5 HOH A 17 317 261 HOH HOH . F 5 HOH A 18 318 288 HOH HOH . F 5 HOH A 19 319 216 HOH HOH . F 5 HOH A 20 320 231 HOH HOH . F 5 HOH A 21 321 282 HOH HOH . F 5 HOH A 22 322 223 HOH HOH . F 5 HOH A 23 323 255 HOH HOH . F 5 HOH A 24 324 269 HOH HOH . F 5 HOH A 25 325 271 HOH HOH . F 5 HOH A 26 326 290 HOH HOH . F 5 HOH A 27 327 275 HOH HOH . F 5 HOH A 28 328 228 HOH HOH . F 5 HOH A 29 329 276 HOH HOH . F 5 HOH A 30 330 233 HOH HOH . F 5 HOH A 31 331 249 HOH HOH . F 5 HOH A 32 332 248 HOH HOH . F 5 HOH A 33 333 285 HOH HOH . F 5 HOH A 34 334 240 HOH HOH . F 5 HOH A 35 335 219 HOH HOH . F 5 HOH A 36 336 222 HOH HOH . F 5 HOH A 37 337 254 HOH HOH . F 5 HOH A 38 338 239 HOH HOH . F 5 HOH A 39 339 245 HOH HOH . F 5 HOH A 40 340 236 HOH HOH . F 5 HOH A 41 341 281 HOH HOH . F 5 HOH A 42 342 232 HOH HOH . F 5 HOH A 43 343 253 HOH HOH . F 5 HOH A 44 344 241 HOH HOH . F 5 HOH A 45 345 247 HOH HOH . F 5 HOH A 46 346 214 HOH HOH . F 5 HOH A 47 347 246 HOH HOH . F 5 HOH A 48 348 252 HOH HOH . F 5 HOH A 49 349 286 HOH HOH . F 5 HOH A 50 350 201 HOH HOH . F 5 HOH A 51 351 202 HOH HOH . F 5 HOH A 52 352 204 HOH HOH . F 5 HOH A 53 353 205 HOH HOH . F 5 HOH A 54 354 207 HOH HOH . F 5 HOH A 55 355 209 HOH HOH . F 5 HOH A 56 356 210 HOH HOH . F 5 HOH A 57 357 211 HOH HOH . F 5 HOH A 58 358 213 HOH HOH . F 5 HOH A 59 359 220 HOH HOH . F 5 HOH A 60 360 221 HOH HOH . F 5 HOH A 61 361 224 HOH HOH . F 5 HOH A 62 362 226 HOH HOH . F 5 HOH A 63 363 227 HOH HOH . F 5 HOH A 64 364 229 HOH HOH . F 5 HOH A 65 365 234 HOH HOH . F 5 HOH A 66 366 235 HOH HOH . F 5 HOH A 67 367 237 HOH HOH . F 5 HOH A 68 368 244 HOH HOH . F 5 HOH A 69 369 251 HOH HOH . F 5 HOH A 70 370 256 HOH HOH . F 5 HOH A 71 371 257 HOH HOH . F 5 HOH A 72 372 260 HOH HOH . F 5 HOH A 73 373 262 HOH HOH . F 5 HOH A 74 374 263 HOH HOH . F 5 HOH A 75 375 264 HOH HOH . F 5 HOH A 76 376 265 HOH HOH . F 5 HOH A 77 377 266 HOH HOH . F 5 HOH A 78 378 277 HOH HOH . F 5 HOH A 79 379 280 HOH HOH . F 5 HOH A 80 380 283 HOH HOH . F 5 HOH A 81 381 292 HOH HOH . F 5 HOH A 82 382 294 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 . . . C 3 4.678 31.079 21.706 1 27.41 ? PG GNP 202 A 1 HETATM 2 O O1G GNP . . . C 3 3.908 31.968 20.761 1 25.12 ? O1G GNP 202 A 1 HETATM 3 O O2G GNP . . . C 3 4.531 31.529 23.144 1 25.79 ? O2G GNP 202 A 1 HETATM 4 O O3G GNP . . . C 3 4.273 29.625 21.731 1 22.36 ? O3G GNP 202 A 1 HETATM 5 N N3B GNP . . . C 3 6.223 31.167 21.302 1 23.19 ? N3B GNP 202 A 1 HETATM 6 P PB GNP . . . C 3 6.854 30.886 19.851 1 21.43 ? PB GNP 202 A 1 HETATM 7 O O1B GNP . . . C 3 6.08 31.65 18.84 1 21.58 ? O1B GNP 202 A 1 HETATM 8 O O2B GNP . . . C 3 6.956 29.426 19.662 1 21.15 ? O2B GNP 202 A 1 HETATM 9 O O3A GNP . . . C 3 8.305 31.423 19.893 1 18.68 ? O3A GNP 202 A 1 HETATM 10 P PA GNP . . . C 3 8.837 32.821 19.469 1 25.1 ? PA GNP 202 A 1 HETATM 11 O O1A GNP . . . C 3 8.867 32.933 17.992 1 22.57 ? O1A GNP 202 A 1 HETATM 12 O O2A GNP . . . C 3 8.13 33.894 20.192 1 23.91 ? O2A GNP 202 A 1 HETATM 13 O O5' GNP . . . C 3 10.356 32.874 19.897 1 22.18 ? O5' GNP 202 A 1 HETATM 14 C C5' GNP . . . C 3 10.815 32.493 21.206 1 25.4 ? C5' GNP 202 A 1 HETATM 15 C C4' GNP . . . C 3 12.195 33.07 21.52 1 25.26 ? C4' GNP 202 A 1 HETATM 16 O O4' GNP . . . C 3 13.278 32.394 20.81 1 21.49 ? O4' GNP 202 A 1 HETATM 17 C C3' GNP . . . C 3 12.384 34.56 21.234 1 29.96 ? C3' GNP 202 A 1 HETATM 18 O O3' GNP . . . C 3 13.325 35.119 22.173 1 27.14 ? O3' GNP 202 A 1 HETATM 19 C C2' GNP . . . C 3 12.943 34.518 19.813 1 25.95 ? C2' GNP 202 A 1 HETATM 20 O O2' GNP . . . C 3 13.648 35.685 19.435 1 29.67 ? O2' GNP 202 A 1 HETATM 21 C C1' GNP . . . C 3 13.866 33.291 19.902 1 26.02 ? C1' GNP 202 A 1 HETATM 22 N N9 GNP . . . C 3 14.011 32.542 18.665 1 24.43 ? N9 GNP 202 A 1 HETATM 23 C C8 GNP . . . C 3 13.019 32.105 17.822 1 22.75 ? C8 GNP 202 A 1 HETATM 24 N N7 GNP . . . C 3 13.486 31.436 16.794 1 22.07 ? N7 GNP 202 A 1 HETATM 25 C C5 GNP . . . C 3 14.86 31.431 16.98 1 21.8 ? C5 GNP 202 A 1 HETATM 26 C C6 GNP . . . C 3 15.895 30.875 16.21 1 23.16 ? C6 GNP 202 A 1 HETATM 27 O O6 GNP . . . C 3 15.807 30.247 15.15 1 25.51 ? O6 GNP 202 A 1 HETATM 28 N N1 GNP . . . C 3 17.149 31.104 16.772 1 26.08 ? N1 GNP 202 A 1 HETATM 29 C C2 GNP . . . C 3 17.372 31.795 17.939 1 26.36 ? C2 GNP 202 A 1 HETATM 30 N N2 GNP . . . C 3 18.642 31.929 18.346 1 27.81 ? N2 GNP 202 A 1 HETATM 31 N N3 GNP . . . C 3 16.413 32.308 18.67 1 25.78 ? N3 GNP 202 A 1 HETATM 32 C C4 GNP . . . C 3 15.192 32.097 18.135 1 25.06 ? C4 GNP 202 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 524 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 32 #