data_2P8X
#
_model_server_result.job_id            sqPkOC44vtSuEBZORgt91w 
_model_server_result.datetime_utc      '2025-07-02 07:01:25' 
_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          2p8x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":843}' 
#
_entry.id    2P8X 
#
_exptl.entry_id    2P8X 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          4 
_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            2P8X 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2P8X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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                      4 
_struct_asym.id                             D 
_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
covale ? covale1 A CG2 ILE 698 T ILE 698 1_555 A CG DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale2 A CA ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
covale ? covale3 A CG2 ILE 698 T ILE 698 1_555 A CAT DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.695 ? 
covale ? covale4 A CB ILE 698 T ILE 698 1_555 A CAT DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
covale ? covale5 A CG2 ILE 698 T ILE 698 1_555 A NE2 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? 
covale ? covale6 A CB ILE 698 T ILE 698 1_555 A CE1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? 
covale ? covale7 A CG2 ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.068 ? 
covale ? covale8 A CB ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.529 ? 
covale ? covale9 A C ILE 698 T ILE 698 1_555 A ND1 DDE 699 T DDE 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
covale ? covale10 A C DDE 699 T DDE 699 1_555 A N ARG 700 T ARG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? 
covale ? covale11 A NE2 DDE 699 T DDE 699 1_555 C C1D APR . T APR 1699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? 
#
_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 236 n n 
PG O2G GNP sing 237 n n 
PG O3G GNP sing 238 n n 
PG N3B GNP sing 239 n n 
O2G HOG2 GNP sing 240 n n 
O3G HOG3 GNP sing 241 n n 
N3B PB GNP sing 242 n n 
N3B HNB3 GNP sing 243 n n 
PB O1B GNP doub 244 n n 
PB O2B GNP sing 245 n n 
PB O3A GNP sing 246 n n 
O2B HOB2 GNP sing 247 n n 
O3A PA GNP sing 248 n n 
PA O1A GNP doub 249 n n 
PA O2A GNP sing 250 n n 
PA O5' GNP sing 251 n n 
O2A HOA2 GNP sing 252 n n 
O5' C5' GNP sing 253 n n 
C5' C4' GNP sing 254 n n 
C5' "H5'2" GNP sing 255 n n 
C5' "H5'1" GNP sing 256 n n 
C4' O4' GNP sing 257 n n 
C4' C3' GNP sing 258 n n 
C4' H4' GNP sing 259 n n 
O4' C1' GNP sing 260 n n 
C3' O3' GNP sing 261 n n 
C3' C2' GNP sing 262 n n 
C3' H3' GNP sing 263 n n 
O3' HO3' GNP sing 264 n n 
C2' O2' GNP sing 265 n n 
C2' C1' GNP sing 266 n n 
C2' H2' GNP sing 267 n n 
O2' HO2' GNP sing 268 n n 
C1' N9 GNP sing 269 n n 
C1' H1' GNP sing 270 n n 
N9 C8 GNP sing 271 n y 
N9 C4 GNP sing 272 n y 
C8 N7 GNP doub 273 n y 
C8 H8 GNP sing 274 n n 
N7 C5 GNP sing 275 n y 
C5 C6 GNP sing 276 n y 
C5 C4 GNP doub 277 n y 
C6 O6 GNP doub 278 n n 
C6 N1 GNP sing 279 n y 
N1 C2 GNP sing 280 n y 
N1 HN1 GNP sing 281 n n 
C2 N2 GNP sing 282 n n 
C2 N3 GNP doub 283 n y 
N2 HN21 GNP sing 284 n n 
N2 HN22 GNP sing 285 n n 
N3 C4 GNP sing 286 n y 
#
_atom_sites.entry_id                     2P8X 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
C 3 APR T 1 1699 1699 APR APR . 
D 4 GNP T 1 843 843 GNP GNP . 
#
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 . . . D 4 -15.176 46.885 -61.941 1 11.41 ? PG GNP 843 T 1 
HETATM 2 O O1G GNP . . . D 4 -14.554 46.069 -60.871 1 14.08 ? O1G GNP 843 T 1 
HETATM 3 O O2G GNP . . . D 4 -15.996 46.198 -63.022 1 24.4 ? O2G GNP 843 T 1 
HETATM 4 O O3G GNP . . . D 4 -16.026 48.081 -61.515 1 10.93 ? O3G GNP 843 T 1 
HETATM 5 N N3B GNP . . . D 4 -14.172 47.903 -62.588 1 10.02 ? N3B GNP 843 T 1 
HETATM 6 P PB GNP . . . D 4 -13.968 48.987 -63.686 1 21.4 ? PB GNP 843 T 1 
HETATM 7 O O1B GNP . . . D 4 -14.721 48.851 -64.916 1 10.46 ? O1B GNP 843 T 1 
HETATM 8 O O2B GNP . . . D 4 -14.256 50.318 -62.961 1 26.12 ? O2B GNP 843 T 1 
HETATM 9 O O3A GNP . . . D 4 -12.492 49.246 -64.119 1 12.87 ? O3A GNP 843 T 1 
HETATM 10 P PA GNP . . . D 4 -11.45 50.29 -63.681 1 2 ? PA GNP 843 T 1 
HETATM 11 O O1A GNP . . . D 4 -11.079 50.088 -62.264 1 10.31 ? O1A GNP 843 T 1 
HETATM 12 O O2A GNP . . . D 4 -11.807 51.681 -63.901 1 11.51 ? O2A GNP 843 T 1 
HETATM 13 O O5' GNP . . . D 4 -10.223 50.142 -64.661 1 8.47 ? O5' GNP 843 T 1 
HETATM 14 C C5' GNP . . . D 4 -9.69 48.81 -64.725 1 17.04 ? C5' GNP 843 T 1 
HETATM 15 C C4' GNP . . . D 4 -8.24 48.743 -65.216 1 17.78 ? C4' GNP 843 T 1 
HETATM 16 O O4' GNP . . . D 4 -8.184 49.203 -66.532 1 21.91 ? O4' GNP 843 T 1 
HETATM 17 C C3' GNP . . . D 4 -7.39 49.739 -64.515 1 17.01 ? C3' GNP 843 T 1 
HETATM 18 O O3' GNP . . . D 4 -6.122 49.169 -64.279 1 24.76 ? O3' GNP 843 T 1 
HETATM 19 C C2' GNP . . . D 4 -7.299 50.933 -65.397 1 18.13 ? C2' GNP 843 T 1 
HETATM 20 O O2' GNP . . . D 4 -6.028 51.573 -65.235 1 21.15 ? O2' GNP 843 T 1 
HETATM 21 C C1' GNP . . . D 4 -7.394 50.362 -66.685 1 13.44 ? C1' GNP 843 T 1 
HETATM 22 N N9 GNP . . . D 4 -7.981 51.318 -67.6 1 3.7 ? N9 GNP 843 T 1 
HETATM 23 C C8 GNP . . . D 4 -9.057 52.13 -67.535 1 7.9 ? C8 GNP 843 T 1 
HETATM 24 N N7 GNP . . . D 4 -9.247 52.888 -68.583 1 2.12 ? N7 GNP 843 T 1 
HETATM 25 C C5 GNP . . . D 4 -8.167 52.522 -69.384 1 11.98 ? C5 GNP 843 T 1 
HETATM 26 C C6 GNP . . . D 4 -7.777 52.968 -70.661 1 15.74 ? C6 GNP 843 T 1 
HETATM 27 O O6 GNP . . . D 4 -8.274 53.878 -71.309 1 20.74 ? O6 GNP 843 T 1 
HETATM 28 N N1 GNP . . . D 4 -6.653 52.313 -71.152 1 15.25 ? N1 GNP 843 T 1 
HETATM 29 C C2 GNP . . . D 4 -5.974 51.338 -70.472 1 22.71 ? C2 GNP 843 T 1 
HETATM 30 N N2 GNP . . . D 4 -4.958 50.767 -71.115 1 22.46 ? N2 GNP 843 T 1 
HETATM 31 N N3 GNP . . . D 4 -6.321 50.923 -69.257 1 14.97 ? N3 GNP 843 T 1 
HETATM 32 C C4 GNP . . . D 4 -7.424 51.56 -68.787 1 9.41 ? C4 GNP 843 T 1 
#
_model_server_stats.io_time_ms              76 
_model_server_stats.parse_time_ms           62 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           32 
#