data_7KFZ
#
_model_server_result.job_id            m-ujx5A-yw3i4zcK5IQAEg 
_model_server_result.datetime_utc      '2025-03-26 17:53:50' 
_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          7kfz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    7KFZ 
#
_exptl.entry_id    7KFZ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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            7KFZ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KFZ 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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    ? 
_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                             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
metalc ? metalc1 C OG SER 18 C SER 17 1_555 E MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? 
metalc ? metalc2 C OG1 THR 36 C THR 35 1_555 E MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? 
metalc ? metalc3 D O1G GNP . C GNP 201 1_555 E MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc4 D O2B GNP . C GNP 201 1_555 E MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
#
_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                     7KFZ 
_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
D 3 GNP C 1 201 201 GNP GNP . 
E 4 MG C 1 202 202 MG MG . 
#
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 3 86.948 121.513 121.411 1 43.46 ? PG GNP 201 C 1 
HETATM 2 O O1G GNP . . . D 3 87.061 120.236 120.65 1 43.46 ? O1G GNP 201 C 1 
HETATM 3 O O2G GNP . . . D 3 88.324 121.916 121.901 1 43.46 ? O2G GNP 201 C 1 
HETATM 4 O O3G GNP . . . D 3 85.996 121.365 122.615 1 43.46 ? O3G GNP 201 C 1 
HETATM 5 N N3B GNP . . . D 3 86.373 122.717 120.375 1 43.46 ? N3B GNP 201 C 1 
HETATM 6 P PB GNP . . . D 3 87.328 122.993 119.095 1 43.46 ? PB GNP 201 C 1 
HETATM 7 O O1B GNP . . . D 3 88.636 123.54 119.578 1 43.46 ? O1B GNP 201 C 1 
HETATM 8 O O2B GNP . . . D 3 87.533 121.671 118.424 1 43.46 ? O2B GNP 201 C 1 
HETATM 9 O O3A GNP . . . D 3 86.628 124.035 118.053 1 43.46 ? O3A GNP 201 C 1 
HETATM 10 P PA GNP . . . D 3 86.016 123.527 116.692 1 43.46 ? PA GNP 201 C 1 
HETATM 11 O O1A GNP . . . D 3 87.095 123.682 115.629 1 43.46 ? O1A GNP 201 C 1 
HETATM 12 O O2A GNP . . . D 3 85.422 122.211 116.819 1 43.46 ? O2A GNP 201 C 1 
HETATM 13 O O5' GNP . . . D 3 84.897 124.553 116.388 1 43.46 ? O5' GNP 201 C 1 
HETATM 14 C C5' GNP . . . D 3 84.954 125.894 116.909 1 43.46 ? C5' GNP 201 C 1 
HETATM 15 C C4' GNP . . . D 3 83.77 126.642 116.369 1 43.46 ? C4' GNP 201 C 1 
HETATM 16 O O4' GNP . . . D 3 84.217 127.885 115.794 1 43.46 ? O4' GNP 201 C 1 
HETATM 17 C C3' GNP . . . D 3 83.032 125.941 115.241 1 43.46 ? C3' GNP 201 C 1 
HETATM 18 O O3' GNP . . . D 3 81.723 126.479 115.138 1 43.46 ? O3' GNP 201 C 1 
HETATM 19 C C2' GNP . . . D 3 83.846 126.364 114.027 1 43.46 ? C2' GNP 201 C 1 
HETATM 20 O O2' GNP . . . D 3 83.043 126.315 112.858 1 43.46 ? O2' GNP 201 C 1 
HETATM 21 C C1' GNP . . . D 3 84.14 127.817 114.382 1 43.46 ? C1' GNP 201 C 1 
HETATM 22 N N9 GNP . . . D 3 85.398 128.323 113.832 1 43.46 ? N9 GNP 201 C 1 
HETATM 23 C C8 GNP . . . D 3 86.636 127.781 113.949 1 43.46 ? C8 GNP 201 C 1 
HETATM 24 N N7 GNP . . . D 3 87.558 128.489 113.349 1 43.46 ? N7 GNP 201 C 1 
HETATM 25 C C5 GNP . . . D 3 86.871 129.562 112.82 1 43.46 ? C5 GNP 201 C 1 
HETATM 26 C C6 GNP . . . D 3 87.332 130.691 112.051 1 43.46 ? C6 GNP 201 C 1 
HETATM 27 O O6 GNP . . . D 3 88.471 130.93 111.701 1 43.46 ? O6 GNP 201 C 1 
HETATM 28 N N1 GNP . . . D 3 86.308 131.543 111.722 1 43.46 ? N1 GNP 201 C 1 
HETATM 29 C C2 GNP . . . D 3 85 131.361 112.065 1 43.46 ? C2 GNP 201 C 1 
HETATM 30 N N2 GNP . . . D 3 84.135 132.288 111.659 1 43.46 ? N2 GNP 201 C 1 
HETATM 31 N N3 GNP . . . D 3 84.567 130.326 112.774 1 43.46 ? N3 GNP 201 C 1 
HETATM 32 C C4 GNP . . . D 3 85.551 129.473 113.108 1 43.46 ? C4 GNP 201 C 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           32 
#