data_9B4Q # _model_server_result.job_id uvGHfn34LNclVo0Do84tYg _model_server_result.datetime_utc '2025-01-22 12:55:48' _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 9b4q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 9B4Q # _exptl.entry_id 9B4Q _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 90 _cell.entry_id 9B4Q _cell.length_a 39.299 _cell.length_b 62.797 _cell.length_c 66.089 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9B4Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _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 _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 18 A SER 28 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc2 A OG1 THR 36 A THR 46 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc3 B O2G GNP . A GNP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc4 B O1B GNP . A GNP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? # _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 9B4Q _atom_sites.fract_transf_matrix[1][1] 0.025446 _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] 0.015924 _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] 0.015131 _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 1 201 300 GNP GNP . C 3 MG A 1 202 1 MG MG . D 4 HOH A 1 301 78 HOH HOH . D 4 HOH A 2 302 146 HOH HOH . D 4 HOH A 3 303 174 HOH HOH . D 4 HOH A 4 304 80 HOH HOH . D 4 HOH A 5 305 79 HOH HOH . D 4 HOH A 6 306 46 HOH HOH . D 4 HOH A 7 307 106 HOH HOH . D 4 HOH A 8 308 49 HOH HOH . D 4 HOH A 9 309 173 HOH HOH . D 4 HOH A 10 310 133 HOH HOH . D 4 HOH A 11 311 141 HOH HOH . D 4 HOH A 12 312 103 HOH HOH . D 4 HOH A 13 313 44 HOH HOH . D 4 HOH A 14 314 139 HOH HOH . D 4 HOH A 15 315 38 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 70 HOH HOH . D 4 HOH A 18 318 93 HOH HOH . D 4 HOH A 19 319 125 HOH HOH . D 4 HOH A 20 320 67 HOH HOH . D 4 HOH A 21 321 148 HOH HOH . D 4 HOH A 22 322 32 HOH HOH . D 4 HOH A 23 323 28 HOH HOH . D 4 HOH A 24 324 169 HOH HOH . D 4 HOH A 25 325 5 HOH HOH . D 4 HOH A 26 326 24 HOH HOH . D 4 HOH A 27 327 60 HOH HOH . D 4 HOH A 28 328 116 HOH HOH . D 4 HOH A 29 329 39 HOH HOH . D 4 HOH A 30 330 100 HOH HOH . D 4 HOH A 31 331 51 HOH HOH . D 4 HOH A 32 332 122 HOH HOH . D 4 HOH A 33 333 73 HOH HOH . D 4 HOH A 34 334 26 HOH HOH . D 4 HOH A 35 335 104 HOH HOH . D 4 HOH A 36 336 33 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 1 HOH HOH . D 4 HOH A 39 339 2 HOH HOH . D 4 HOH A 40 340 43 HOH HOH . D 4 HOH A 41 341 9 HOH HOH . D 4 HOH A 42 342 53 HOH HOH . D 4 HOH A 43 343 65 HOH HOH . D 4 HOH A 44 344 8 HOH HOH . D 4 HOH A 45 345 81 HOH HOH . D 4 HOH A 46 346 3 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 21 HOH HOH . D 4 HOH A 49 349 7 HOH HOH . D 4 HOH A 50 350 20 HOH HOH . D 4 HOH A 51 351 95 HOH HOH . D 4 HOH A 52 352 92 HOH HOH . D 4 HOH A 53 353 31 HOH HOH . D 4 HOH A 54 354 6 HOH HOH . D 4 HOH A 55 355 35 HOH HOH . D 4 HOH A 56 356 63 HOH HOH . D 4 HOH A 57 357 111 HOH HOH . D 4 HOH A 58 358 86 HOH HOH . D 4 HOH A 59 359 109 HOH HOH . D 4 HOH A 60 360 62 HOH HOH . D 4 HOH A 61 361 159 HOH HOH . D 4 HOH A 62 362 110 HOH HOH . D 4 HOH A 63 363 19 HOH HOH . D 4 HOH A 64 364 4 HOH HOH . D 4 HOH A 65 365 101 HOH HOH . D 4 HOH A 66 366 11 HOH HOH . D 4 HOH A 67 367 56 HOH HOH . D 4 HOH A 68 368 45 HOH HOH . D 4 HOH A 69 369 114 HOH HOH . D 4 HOH A 70 370 30 HOH HOH . D 4 HOH A 71 371 58 HOH HOH . D 4 HOH A 72 372 66 HOH HOH . D 4 HOH A 73 373 42 HOH HOH . D 4 HOH A 74 374 129 HOH HOH . D 4 HOH A 75 375 54 HOH HOH . D 4 HOH A 76 376 61 HOH HOH . D 4 HOH A 77 377 136 HOH HOH . D 4 HOH A 78 378 99 HOH HOH . D 4 HOH A 79 379 41 HOH HOH . D 4 HOH A 80 380 29 HOH HOH . D 4 HOH A 81 381 94 HOH HOH . D 4 HOH A 82 382 25 HOH HOH . D 4 HOH A 83 383 108 HOH HOH . D 4 HOH A 84 384 147 HOH HOH . D 4 HOH A 85 385 87 HOH HOH . D 4 HOH A 86 386 10 HOH HOH . D 4 HOH A 87 387 155 HOH HOH . D 4 HOH A 88 388 50 HOH HOH . D 4 HOH A 89 389 77 HOH HOH . D 4 HOH A 90 390 59 HOH HOH . D 4 HOH A 91 391 132 HOH HOH . D 4 HOH A 92 392 14 HOH HOH . D 4 HOH A 93 393 69 HOH HOH . D 4 HOH A 94 394 160 HOH HOH . D 4 HOH A 95 395 154 HOH HOH . D 4 HOH A 96 396 22 HOH HOH . D 4 HOH A 97 397 52 HOH HOH . D 4 HOH A 98 398 36 HOH HOH . D 4 HOH A 99 399 40 HOH HOH . D 4 HOH A 100 400 12 HOH HOH . D 4 HOH A 101 401 17 HOH HOH . D 4 HOH A 102 402 150 HOH HOH . D 4 HOH A 103 403 161 HOH HOH . D 4 HOH A 104 404 115 HOH HOH . D 4 HOH A 105 405 23 HOH HOH . D 4 HOH A 106 406 143 HOH HOH . D 4 HOH A 107 407 55 HOH HOH . D 4 HOH A 108 408 57 HOH HOH . D 4 HOH A 109 409 84 HOH HOH . D 4 HOH A 110 410 18 HOH HOH . D 4 HOH A 111 411 144 HOH HOH . D 4 HOH A 112 412 82 HOH HOH . D 4 HOH A 113 413 112 HOH HOH . D 4 HOH A 114 414 118 HOH HOH . D 4 HOH A 115 415 68 HOH HOH . D 4 HOH A 116 416 64 HOH HOH . D 4 HOH A 117 417 71 HOH HOH . D 4 HOH A 118 418 27 HOH HOH . D 4 HOH A 119 419 172 HOH HOH . D 4 HOH A 120 420 107 HOH HOH . D 4 HOH A 121 421 149 HOH HOH . D 4 HOH A 122 422 13 HOH HOH . D 4 HOH A 123 423 72 HOH HOH . D 4 HOH A 124 424 105 HOH HOH . D 4 HOH A 125 425 168 HOH HOH . D 4 HOH A 126 426 74 HOH HOH . D 4 HOH A 127 427 156 HOH HOH . D 4 HOH A 128 428 85 HOH HOH . D 4 HOH A 129 429 102 HOH HOH . D 4 HOH A 130 430 152 HOH HOH . D 4 HOH A 131 431 96 HOH HOH . D 4 HOH A 132 432 123 HOH HOH . D 4 HOH A 133 433 75 HOH HOH . D 4 HOH A 134 434 98 HOH HOH . D 4 HOH A 135 435 153 HOH HOH . D 4 HOH A 136 436 120 HOH HOH . D 4 HOH A 137 437 137 HOH HOH . D 4 HOH A 138 438 140 HOH HOH . D 4 HOH A 139 439 34 HOH HOH . D 4 HOH A 140 440 89 HOH HOH . D 4 HOH A 141 441 128 HOH HOH . D 4 HOH A 142 442 131 HOH HOH . D 4 HOH A 143 443 145 HOH HOH . D 4 HOH A 144 444 162 HOH HOH . D 4 HOH A 145 445 158 HOH HOH . D 4 HOH A 146 446 15 HOH HOH . D 4 HOH A 147 447 97 HOH HOH . D 4 HOH A 148 448 170 HOH HOH . D 4 HOH A 149 449 166 HOH HOH . D 4 HOH A 150 450 127 HOH HOH . D 4 HOH A 151 451 88 HOH HOH . D 4 HOH A 152 452 126 HOH HOH . D 4 HOH A 153 453 91 HOH HOH . D 4 HOH A 154 454 151 HOH HOH . D 4 HOH A 155 455 83 HOH HOH . D 4 HOH A 156 456 134 HOH HOH . D 4 HOH A 157 457 135 HOH HOH . D 4 HOH A 158 458 119 HOH HOH . D 4 HOH A 159 459 113 HOH HOH . D 4 HOH A 160 460 90 HOH HOH . D 4 HOH A 161 461 142 HOH HOH . D 4 HOH A 162 462 138 HOH HOH . D 4 HOH A 163 463 163 HOH HOH . D 4 HOH A 164 464 164 HOH HOH . D 4 HOH A 165 465 165 HOH HOH . D 4 HOH A 166 466 117 HOH HOH . D 4 HOH A 167 467 76 HOH HOH . D 4 HOH A 168 468 130 HOH HOH . D 4 HOH A 169 469 48 HOH HOH . D 4 HOH A 170 470 124 HOH HOH . D 4 HOH A 171 471 157 HOH HOH . D 4 HOH A 172 472 121 HOH HOH . D 4 HOH A 173 473 167 HOH HOH . D 4 HOH A 174 474 171 HOH HOH . D 4 HOH A 175 475 175 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 -20.133 16.042 -21.782 1 23.25 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . B 2 -21.59 15.792 -22.123 1 23.02 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . B 2 -19.372 16.462 -23.021 1 22.42 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . B 2 -19.542 14.811 -21.109 1 23.88 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . B 2 -20.208 17.356 -20.633 1 22.4 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . B 2 -18.735 18.066 -20.127 1 20.72 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . B 2 -17.908 18.376 -21.373 1 19.33 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . B 2 -18.07 17.236 -19.071 1 21.11 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . B 2 -19.243 19.448 -19.405 1 19.58 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . B 2 -19.322 20.915 -20.061 1 20.75 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . B 2 -17.917 21.362 -20.199 1 21.35 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . B 2 -20.124 20.952 -21.331 1 21.76 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . B 2 -19.99 21.649 -18.842 1 21.27 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . B 2 -21.315 21.27 -18.488 1 19.57 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . B 2 -21.985 22.402 -17.713 1 26.43 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . B 2 -21.245 22.692 -16.512 1 23.59 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . B 2 -22.035 23.797 -18.325 1 24.44 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . B 2 -23.288 24.467 -18.381 1 25.75 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . B 2 -20.794 24.564 -17.997 1 24.28 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . B 2 -20.995 25.979 -17.964 1 24.31 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . B 2 -20.661 24.022 -16.626 1 21.87 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . B 2 -19.365 24.158 -15.968 1 23.67 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . B 2 -18.258 23.516 -16.419 1 22.08 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . B 2 -17.209 23.77 -15.631 1 24.15 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . B 2 -17.649 24.57 -14.636 1 22.91 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . B 2 -17.063 25.183 -13.433 1 23.72 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . B 2 -15.838 25.029 -13.185 1 23.79 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . B 2 -17.891 25.924 -12.666 1 22.4 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . B 2 -19.208 26.138 -12.893 1 26.88 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . B 2 -19.877 26.933 -12.021 1 27.6 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . B 2 -19.827 25.605 -13.984 1 28.11 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . B 2 -19.101 24.816 -14.838 1 23.13 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 459 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #