data_1YZN # _model_server_result.job_id lhrmNl3w1EQrYZYex92KJg _model_server_result.datetime_utc '2024-11-16 07:19:17' _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 1yzn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 1YZN # _exptl.entry_id 1YZN _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 90 _cell.entry_id 1YZN _cell.length_a 39.011 _cell.length_b 56.93 _cell.length_c 74.72 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YZN _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_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 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 35 A SER 22 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc2 A OG1 THR 53 A THR 40 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc3 C O2G GNP . A GNP 300 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc4 C O2B GNP . A GNP 300 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 B MG MG . A MG 301 1_555 D O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc6 B MG MG . A MG 301 1_555 D O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _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 1YZN _atom_sites.fract_transf_matrix[1][1] 0.025634 _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] 0.017565 _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] 0.013383 _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 1 301 201 MG MG . C 3 GNP A 1 300 200 GNP GNP . D 4 HOH A 1 302 1 HOH HOH . D 4 HOH A 2 303 2 HOH HOH . D 4 HOH A 3 304 3 HOH HOH . D 4 HOH A 4 305 4 HOH HOH . D 4 HOH A 5 306 5 HOH HOH . D 4 HOH A 6 307 6 HOH HOH . D 4 HOH A 7 308 8 HOH HOH . D 4 HOH A 8 309 9 HOH HOH . D 4 HOH A 9 310 10 HOH HOH . D 4 HOH A 10 311 14 HOH HOH . D 4 HOH A 11 312 15 HOH HOH . D 4 HOH A 12 313 16 HOH HOH . D 4 HOH A 13 314 17 HOH HOH . D 4 HOH A 14 315 18 HOH HOH . D 4 HOH A 15 316 20 HOH HOH . D 4 HOH A 16 317 21 HOH HOH . D 4 HOH A 17 318 22 HOH HOH . D 4 HOH A 18 319 24 HOH HOH . D 4 HOH A 19 320 25 HOH HOH . D 4 HOH A 20 321 26 HOH HOH . D 4 HOH A 21 322 27 HOH HOH . D 4 HOH A 22 323 28 HOH HOH . D 4 HOH A 23 324 29 HOH HOH . D 4 HOH A 24 325 31 HOH HOH . D 4 HOH A 25 326 32 HOH HOH . D 4 HOH A 26 327 33 HOH HOH . D 4 HOH A 27 328 35 HOH HOH . D 4 HOH A 28 329 37 HOH HOH . D 4 HOH A 29 330 38 HOH HOH . D 4 HOH A 30 331 39 HOH HOH . D 4 HOH A 31 332 40 HOH HOH . D 4 HOH A 32 333 41 HOH HOH . D 4 HOH A 33 334 42 HOH HOH . D 4 HOH A 34 335 43 HOH HOH . D 4 HOH A 35 336 44 HOH HOH . D 4 HOH A 36 337 45 HOH HOH . D 4 HOH A 37 338 46 HOH HOH . D 4 HOH A 38 339 48 HOH HOH . D 4 HOH A 39 340 49 HOH HOH . D 4 HOH A 40 341 50 HOH HOH . D 4 HOH A 41 342 53 HOH HOH . D 4 HOH A 42 343 54 HOH HOH . D 4 HOH A 43 344 55 HOH HOH . D 4 HOH A 44 345 56 HOH HOH . D 4 HOH A 45 346 57 HOH HOH . D 4 HOH A 46 347 59 HOH HOH . D 4 HOH A 47 348 60 HOH HOH . D 4 HOH A 48 349 61 HOH HOH . D 4 HOH A 49 350 63 HOH HOH . D 4 HOH A 50 351 64 HOH HOH . D 4 HOH A 51 352 65 HOH HOH . D 4 HOH A 52 353 67 HOH HOH . D 4 HOH A 53 354 68 HOH HOH . D 4 HOH A 54 355 69 HOH HOH . D 4 HOH A 55 356 70 HOH HOH . D 4 HOH A 56 357 71 HOH HOH . D 4 HOH A 57 358 72 HOH HOH . D 4 HOH A 58 359 75 HOH HOH . D 4 HOH A 59 360 76 HOH HOH . D 4 HOH A 60 361 77 HOH HOH . D 4 HOH A 61 362 78 HOH HOH . D 4 HOH A 62 363 79 HOH HOH . D 4 HOH A 63 364 80 HOH HOH . D 4 HOH A 64 365 81 HOH HOH . D 4 HOH A 65 366 82 HOH HOH . D 4 HOH A 66 367 84 HOH HOH . D 4 HOH A 67 368 85 HOH HOH . D 4 HOH A 68 369 86 HOH HOH . D 4 HOH A 69 370 87 HOH HOH . D 4 HOH A 70 371 88 HOH HOH . D 4 HOH A 71 372 89 HOH HOH . D 4 HOH A 72 373 90 HOH HOH . D 4 HOH A 73 374 91 HOH HOH . D 4 HOH A 74 375 92 HOH HOH . D 4 HOH A 75 376 93 HOH HOH . D 4 HOH A 76 377 94 HOH HOH . D 4 HOH A 77 378 96 HOH HOH . D 4 HOH A 78 379 97 HOH HOH . D 4 HOH A 79 380 99 HOH HOH . D 4 HOH A 80 381 100 HOH HOH . D 4 HOH A 81 382 102 HOH HOH . D 4 HOH A 82 383 103 HOH HOH . D 4 HOH A 83 384 105 HOH HOH . D 4 HOH A 84 385 106 HOH HOH . D 4 HOH A 85 386 107 HOH HOH . D 4 HOH A 86 387 108 HOH HOH . D 4 HOH A 87 388 110 HOH HOH . D 4 HOH A 88 389 111 HOH HOH . D 4 HOH A 89 390 112 HOH HOH . D 4 HOH A 90 391 113 HOH HOH . D 4 HOH A 91 392 114 HOH HOH . D 4 HOH A 92 393 115 HOH HOH . D 4 HOH A 93 394 116 HOH HOH . D 4 HOH A 94 395 117 HOH HOH . D 4 HOH A 95 396 118 HOH HOH . D 4 HOH A 96 397 120 HOH HOH . D 4 HOH A 97 398 121 HOH HOH . D 4 HOH A 98 399 123 HOH HOH . D 4 HOH A 99 400 124 HOH HOH . D 4 HOH A 100 401 126 HOH HOH . D 4 HOH A 101 402 127 HOH HOH . D 4 HOH A 102 403 129 HOH HOH . D 4 HOH A 103 404 130 HOH HOH . D 4 HOH A 104 405 131 HOH HOH . D 4 HOH A 105 406 132 HOH HOH . D 4 HOH A 106 407 133 HOH HOH . D 4 HOH A 107 408 136 HOH HOH . D 4 HOH A 108 409 137 HOH HOH . D 4 HOH A 109 410 140 HOH HOH . D 4 HOH A 110 411 141 HOH HOH . D 4 HOH A 111 412 142 HOH HOH . D 4 HOH A 112 413 143 HOH HOH . D 4 HOH A 113 414 144 HOH HOH . D 4 HOH A 114 415 146 HOH HOH . D 4 HOH A 115 416 147 HOH HOH . D 4 HOH A 116 417 150 HOH HOH . D 4 HOH A 117 418 151 HOH HOH . D 4 HOH A 118 419 152 HOH HOH . D 4 HOH A 119 420 153 HOH HOH . D 4 HOH A 120 421 155 HOH HOH . D 4 HOH A 121 422 156 HOH HOH . D 4 HOH A 122 423 157 HOH HOH . D 4 HOH A 123 424 158 HOH HOH . D 4 HOH A 124 425 159 HOH HOH . D 4 HOH A 125 426 161 HOH HOH . D 4 HOH A 126 427 164 HOH HOH . D 4 HOH A 127 428 165 HOH HOH . D 4 HOH A 128 429 167 HOH HOH . D 4 HOH A 129 430 169 HOH HOH . D 4 HOH A 130 431 170 HOH HOH . D 4 HOH A 131 432 171 HOH HOH . D 4 HOH A 132 433 172 HOH HOH . D 4 HOH A 133 434 173 HOH HOH . D 4 HOH A 134 435 175 HOH HOH . D 4 HOH A 135 436 176 HOH HOH . D 4 HOH A 136 437 177 HOH HOH . D 4 HOH A 137 438 181 HOH HOH . D 4 HOH A 138 439 183 HOH HOH . D 4 HOH A 139 440 184 HOH HOH . D 4 HOH A 140 441 185 HOH HOH . D 4 HOH A 141 442 186 HOH HOH . D 4 HOH A 142 443 188 HOH HOH . D 4 HOH A 143 444 191 HOH HOH . D 4 HOH A 144 445 192 HOH HOH . D 4 HOH A 145 446 193 HOH HOH . D 4 HOH A 146 447 195 HOH HOH . D 4 HOH A 147 448 196 HOH HOH . D 4 HOH A 148 449 198 HOH HOH . D 4 HOH A 149 450 199 HOH HOH . D 4 HOH A 150 451 200 HOH HOH . D 4 HOH A 151 452 201 HOH HOH . D 4 HOH A 152 453 203 HOH HOH . D 4 HOH A 153 454 204 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 3.461 22.255 10.801 1 15.1 ? PG GNP 300 A 1 HETATM 2 O O1G GNP . . . C 3 2.267 21.583 11.426 1 12.95 ? O1G GNP 300 A 1 HETATM 3 O O2G GNP . . . C 3 3.326 22.697 9.367 1 13 ? O2G GNP 300 A 1 HETATM 4 O O3G GNP . . . C 3 4.606 21.318 11.076 1 15.23 ? O3G GNP 300 A 1 HETATM 5 N N3B GNP . . . C 3 3.722 23.604 11.639 1 13.89 ? N3B GNP 300 A 1 HETATM 6 P PB GNP . . . C 3 4.927 24.632 11.424 1 15.52 ? PB GNP 300 A 1 HETATM 7 O O1B GNP . . . C 3 6.13 24.129 12.13 1 15.62 ? O1B GNP 300 A 1 HETATM 8 O O2B GNP . . . C 3 5.065 24.969 9.987 1 15.1 ? O2B GNP 300 A 1 HETATM 9 O O3A GNP . . . C 3 4.567 25.967 12.113 1 16.34 ? O3A GNP 300 A 1 HETATM 10 P PA GNP . . . C 3 3.808 27.174 11.511 1 16.94 ? PA GNP 300 A 1 HETATM 11 O O1A GNP . . . C 3 4.721 28.024 10.719 1 15.9 ? O1A GNP 300 A 1 HETATM 12 O O2A GNP . . . C 3 2.556 26.748 10.875 1 16.72 ? O2A GNP 300 A 1 HETATM 13 O O5' GNP . . . C 3 3.434 28.065 12.767 1 17.62 ? O5' GNP 300 A 1 HETATM 14 C C5' GNP . . . C 3 2.692 27.517 13.864 1 18.21 ? C5' GNP 300 A 1 HETATM 15 C C4' GNP . . . C 3 2.02 28.619 14.663 1 18.8 ? C4' GNP 300 A 1 HETATM 16 O O4' GNP . . . C 3 3.006 29.384 15.409 1 18.6 ? O4' GNP 300 A 1 HETATM 17 C C3' GNP . . . C 3 1.238 29.648 13.857 1 20.13 ? C3' GNP 300 A 1 HETATM 18 O O3' GNP . . . C 3 0.118 30.077 14.631 1 20.57 ? O3' GNP 300 A 1 HETATM 19 C C2' GNP . . . C 3 2.259 30.759 13.645 1 19.63 ? C2' GNP 300 A 1 HETATM 20 O O2' GNP . . . C 3 1.656 32.024 13.434 1 19.55 ? O2' GNP 300 A 1 HETATM 21 C C1' GNP . . . C 3 3.03 30.722 14.967 1 19.57 ? C1' GNP 300 A 1 HETATM 22 N N9 GNP . . . C 3 4.414 31.203 14.853 1 19.46 ? N9 GNP 300 A 1 HETATM 23 C C8 GNP . . . C 3 5.347 30.822 13.914 1 19.65 ? C8 GNP 300 A 1 HETATM 24 N N7 GNP . . . C 3 6.497 31.422 14.034 1 19.37 ? N7 GNP 300 A 1 HETATM 25 C C5 GNP . . . C 3 6.319 32.256 15.135 1 19.55 ? C5 GNP 300 A 1 HETATM 26 C C6 GNP . . . C 3 7.22 33.163 15.746 1 19.7 ? C6 GNP 300 A 1 HETATM 27 O O6 GNP . . . C 3 8.394 33.402 15.422 1 19.83 ? O6 GNP 300 A 1 HETATM 28 N N1 GNP . . . C 3 6.652 33.826 16.84 1 19.66 ? N1 GNP 300 A 1 HETATM 29 C C2 GNP . . . C 3 5.361 33.644 17.283 1 19.64 ? C2 GNP 300 A 1 HETATM 30 N N2 GNP . . . C 3 4.99 34.367 18.356 1 19.55 ? N2 GNP 300 A 1 HETATM 31 N N3 GNP . . . C 3 4.509 32.79 16.721 1 19.56 ? N3 GNP 300 A 1 HETATM 32 C C4 GNP . . . C 3 5.043 32.136 15.65 1 19.37 ? C4 GNP 300 A 1 # _model_server_stats.io_time_ms 88 _model_server_stats.parse_time_ms 39 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 1090 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 32 #