data_8YP0
#
_model_server_result.job_id            2uQKrvpvDzbq7XtsHulGUg 
_model_server_result.datetime_utc      '2025-04-27 04:02:36' 
_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          8yp0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    8YP0 
#
_exptl.entry_id    8YP0 
_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            8YP0 
_cell.length_a            40.747 
_cell.length_b            61.71 
_cell.length_c            62.189 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YP0 
_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        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 
_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 18 A SER 23 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? 
metalc ? metalc2 B MG MG . A MG 201 1_555 C O2B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? 
metalc ? metalc3 B MG MG . A MG 201 1_555 C O1G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc4 B MG MG . A MG 201 1_555 D O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc5 B MG MG . A MG 201 1_555 D O HOH . A HOH 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc6 B MG MG . A MG 201 1_555 D O HOH . A HOH 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
#
_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                     8YP0 
_atom_sites.fract_transf_matrix[1][1]    0.024542 
_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]    0.016205 
_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]    0.01608 
_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 1 MG MG . 
C 3 GNP A 1 202 201 GNP GNP . 
D 4 HOH A 1 301 19 HOH HOH . 
D 4 HOH A 2 302 66 HOH HOH . 
D 4 HOH A 3 303 110 HOH HOH . 
D 4 HOH A 4 304 17 HOH HOH . 
D 4 HOH A 5 305 95 HOH HOH . 
D 4 HOH A 6 306 13 HOH HOH . 
D 4 HOH A 7 307 82 HOH HOH . 
D 4 HOH A 8 308 60 HOH HOH . 
D 4 HOH A 9 309 11 HOH HOH . 
D 4 HOH A 10 310 16 HOH HOH . 
D 4 HOH A 11 311 94 HOH HOH . 
D 4 HOH A 12 312 28 HOH HOH . 
D 4 HOH A 13 313 44 HOH HOH . 
D 4 HOH A 14 314 119 HOH HOH . 
D 4 HOH A 15 315 105 HOH HOH . 
D 4 HOH A 16 316 25 HOH HOH . 
D 4 HOH A 17 317 35 HOH HOH . 
D 4 HOH A 18 318 48 HOH HOH . 
D 4 HOH A 19 319 15 HOH HOH . 
D 4 HOH A 20 320 63 HOH HOH . 
D 4 HOH A 21 321 29 HOH HOH . 
D 4 HOH A 22 322 1 HOH HOH . 
D 4 HOH A 23 323 4 HOH HOH . 
D 4 HOH A 24 324 5 HOH HOH . 
D 4 HOH A 25 325 86 HOH HOH . 
D 4 HOH A 26 326 38 HOH HOH . 
D 4 HOH A 27 327 62 HOH HOH . 
D 4 HOH A 28 328 97 HOH HOH . 
D 4 HOH A 29 329 90 HOH HOH . 
D 4 HOH A 30 330 10 HOH HOH . 
D 4 HOH A 31 331 24 HOH HOH . 
D 4 HOH A 32 332 31 HOH HOH . 
D 4 HOH A 33 333 6 HOH HOH . 
D 4 HOH A 34 334 22 HOH HOH . 
D 4 HOH A 35 335 49 HOH HOH . 
D 4 HOH A 36 336 42 HOH HOH . 
D 4 HOH A 37 337 7 HOH HOH . 
D 4 HOH A 38 338 74 HOH HOH . 
D 4 HOH A 39 339 2 HOH HOH . 
D 4 HOH A 40 340 53 HOH HOH . 
D 4 HOH A 41 341 52 HOH HOH . 
D 4 HOH A 42 342 8 HOH HOH . 
D 4 HOH A 43 343 26 HOH HOH . 
D 4 HOH A 44 344 113 HOH HOH . 
D 4 HOH A 45 345 9 HOH HOH . 
D 4 HOH A 46 346 99 HOH HOH . 
D 4 HOH A 47 347 12 HOH HOH . 
D 4 HOH A 48 348 33 HOH HOH . 
D 4 HOH A 49 349 59 HOH HOH . 
D 4 HOH A 50 350 32 HOH HOH . 
D 4 HOH A 51 351 92 HOH HOH . 
D 4 HOH A 52 352 76 HOH HOH . 
D 4 HOH A 53 353 51 HOH HOH . 
D 4 HOH A 54 354 107 HOH HOH . 
D 4 HOH A 55 355 3 HOH HOH . 
D 4 HOH A 56 356 14 HOH HOH . 
D 4 HOH A 57 357 40 HOH HOH . 
D 4 HOH A 58 358 93 HOH HOH . 
D 4 HOH A 59 359 23 HOH HOH . 
D 4 HOH A 60 360 69 HOH HOH . 
D 4 HOH A 61 361 79 HOH HOH . 
D 4 HOH A 62 362 27 HOH HOH . 
D 4 HOH A 63 363 78 HOH HOH . 
D 4 HOH A 64 364 118 HOH HOH . 
D 4 HOH A 65 365 57 HOH HOH . 
D 4 HOH A 66 366 83 HOH HOH . 
D 4 HOH A 67 367 101 HOH HOH . 
D 4 HOH A 68 368 102 HOH HOH . 
D 4 HOH A 69 369 104 HOH HOH . 
D 4 HOH A 70 370 114 HOH HOH . 
D 4 HOH A 71 371 81 HOH HOH . 
D 4 HOH A 72 372 98 HOH HOH . 
D 4 HOH A 73 373 77 HOH HOH . 
D 4 HOH A 74 374 50 HOH HOH . 
D 4 HOH A 75 375 18 HOH HOH . 
D 4 HOH A 76 376 54 HOH HOH . 
D 4 HOH A 77 377 96 HOH HOH . 
D 4 HOH A 78 378 36 HOH HOH . 
D 4 HOH A 79 379 46 HOH HOH . 
D 4 HOH A 80 380 85 HOH HOH . 
D 4 HOH A 81 381 88 HOH HOH . 
D 4 HOH A 82 382 116 HOH HOH . 
D 4 HOH A 83 383 47 HOH HOH . 
D 4 HOH A 84 384 45 HOH HOH . 
D 4 HOH A 85 385 20 HOH HOH . 
D 4 HOH A 86 386 73 HOH HOH . 
D 4 HOH A 87 387 117 HOH HOH . 
D 4 HOH A 88 388 34 HOH HOH . 
D 4 HOH A 89 389 68 HOH HOH . 
D 4 HOH A 90 390 108 HOH HOH . 
D 4 HOH A 91 391 61 HOH HOH . 
D 4 HOH A 92 392 37 HOH HOH . 
D 4 HOH A 93 393 39 HOH HOH . 
D 4 HOH A 94 394 21 HOH HOH . 
D 4 HOH A 95 395 58 HOH HOH . 
D 4 HOH A 96 396 91 HOH HOH . 
D 4 HOH A 97 397 43 HOH HOH . 
D 4 HOH A 98 398 109 HOH HOH . 
D 4 HOH A 99 399 41 HOH HOH . 
D 4 HOH A 100 400 70 HOH HOH . 
D 4 HOH A 101 401 65 HOH HOH . 
D 4 HOH A 102 402 80 HOH HOH . 
D 4 HOH A 103 403 84 HOH HOH . 
D 4 HOH A 104 404 89 HOH HOH . 
D 4 HOH A 105 405 72 HOH HOH . 
D 4 HOH A 106 406 67 HOH HOH . 
D 4 HOH A 107 407 30 HOH HOH . 
D 4 HOH A 108 408 87 HOH HOH . 
D 4 HOH A 109 409 112 HOH HOH . 
D 4 HOH A 110 410 106 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 22.962 -2.501 15.41 1 23.87 ? PG GNP 202 A 1 
HETATM 2 O O1G GNP . . . C 3 23.914 -1.41 15.155 1 22.09 ? O1G GNP 202 A 1 
HETATM 3 O O2G GNP . . . C 3 21.835 -1.913 16.164 1 24.5 -1 O2G GNP 202 A 1 
HETATM 4 O O3G GNP . . . C 3 23.56 -3.665 16.102 1 24.14 -1 O3G GNP 202 A 1 
HETATM 5 N N3B GNP . . . C 3 22.29 -3.04 14.013 1 20.18 ? N3B GNP 202 A 1 
HETATM 6 P PB GNP . . . C 3 21.563 -2.208 12.806 1 20.01 ? PB GNP 202 A 1 
HETATM 7 O O1B GNP . . . C 3 20.21 -1.775 13.208 1 18.54 ? O1B GNP 202 A 1 
HETATM 8 O O2B GNP . . . C 3 22.394 -1.068 12.382 1 19.02 -1 O2B GNP 202 A 1 
HETATM 9 O O3A GNP . . . C 3 21.566 -3.227 11.545 1 17.06 ? O3A GNP 202 A 1 
HETATM 10 P PA GNP . . . C 3 22.587 -3.484 10.341 1 20.09 ? PA GNP 202 A 1 
HETATM 11 O O1A GNP . . . C 3 22.501 -2.358 9.388 1 19.53 ? O1A GNP 202 A 1 
HETATM 12 O O2A GNP . . . C 3 23.907 -3.835 10.918 1 20.72 -1 O2A GNP 202 A 1 
HETATM 13 O O5' GNP . . . C 3 21.926 -4.759 9.648 1 21.2 ? O5' GNP 202 A 1 
HETATM 14 C C5' GNP . . . C 3 21.855 -6.027 10.337 1 18.95 ? C5' GNP 202 A 1 
HETATM 15 C C4' GNP . . . C 3 21.848 -7.137 9.315 1 24.91 ? C4' GNP 202 A 1 
HETATM 16 O O4' GNP . . . C 3 20.634 -7.075 8.528 1 22.13 ? O4' GNP 202 A 1 
HETATM 17 C C3' GNP . . . C 3 23.005 -7.099 8.317 1 19.03 ? C3' GNP 202 A 1 
HETATM 18 O O3' GNP . . . C 3 23.46 -8.413 8.014 1 25.77 ? O3' GNP 202 A 1 
HETATM 19 C C2' GNP . . . C 3 22.376 -6.422 7.096 1 24.26 ? C2' GNP 202 A 1 
HETATM 20 O O2' GNP . . . C 3 23.027 -6.792 5.885 1 24.2 ? O2' GNP 202 A 1 
HETATM 21 C C1' GNP . . . C 3 20.963 -6.99 7.154 1 21.79 ? C1' GNP 202 A 1 
HETATM 22 N N9 GNP . . . C 3 19.949 -6.163 6.483 1 21.77 ? N9 GNP 202 A 1 
HETATM 23 C C8 GNP . . . C 3 19.752 -4.808 6.58 1 19.4 ? C8 GNP 202 A 1 
HETATM 24 N N7 GNP . . . C 3 18.752 -4.377 5.84 1 22.39 ? N7 GNP 202 A 1 
HETATM 25 C C5 GNP . . . C 3 18.266 -5.518 5.221 1 18.56 ? C5 GNP 202 A 1 
HETATM 26 C C6 GNP . . . C 3 17.19 -5.704 4.292 1 24.29 ? C6 GNP 202 A 1 
HETATM 27 O O6 GNP . . . C 3 16.438 -4.842 3.833 1 18.98 ? O6 GNP 202 A 1 
HETATM 28 N N1 GNP . . . C 3 17.049 -7.027 3.921 1 16.94 ? N1 GNP 202 A 1 
HETATM 29 C C2 GNP . . . C 3 17.83 -8.062 4.366 1 25.68 ? C2 GNP 202 A 1 
HETATM 30 N N2 GNP . . . C 3 17.552 -9.278 3.892 1 21.03 ? N2 GNP 202 A 1 
HETATM 31 N N3 GNP . . . C 3 18.832 -7.903 5.226 1 17.44 ? N3 GNP 202 A 1 
HETATM 32 C C4 GNP . . . C 3 18.998 -6.624 5.606 1 18.45 ? C4 GNP 202 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           32 
#