data_7SD0
#
_model_server_result.job_id            0rWerW2i18fRUnE0kdesqA 
_model_server_result.datetime_utc      '2025-08-31 04:08:09' 
_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          7sd0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":500}' 
#
_entry.id    7SD0 
#
_exptl.entry_id    7SD0 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              521.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC 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            7SD0 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7SD0 
_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,F,G 
_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                      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
metalc ? metalc1 B OG SER 29 B SER 27 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc2 B OG1 THR 47 B THR 45 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? 
metalc ? metalc3 D O1G GCP . B GCP 500 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc4 D O2G GCP . B GCP 500 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc5 D O2B GCP . B GCP 500 1_555 E MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc6 C OD2 ASP 66 C ASP 64 1_555 G MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? 
metalc ? metalc7 C OD2 ASP 94 C ASP 92 1_555 F MN MN . C MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc8 C OD2 ASP 94 C ASP 92 1_555 G MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc9 C OD1 ASN 126 C ASN 124 1_555 F MN MN . C MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? 
metalc ? metalc10 C NE2 HIS 175 C HIS 173 1_555 F MN MN . C MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc11 C ND1 HIS 250 C HIS 248 1_555 F MN MN . C MN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc12 C O HIS 250 C HIS 248 1_555 G MN MN . C MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? 
#
_chem_comp.formula           'C11 H18 N5 O13 P3' 
_chem_comp.formula_weight    521.208 
_chem_comp.id                GCP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOMETHYLPHOSPHONIC 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 GCP doub 83 n n 
PG O2G GCP sing 84 n n 
PG O3G GCP sing 85 n n 
PG C3B GCP sing 86 n n 
O2G HOG2 GCP sing 87 n n 
O3G HOG3 GCP sing 88 n n 
C3B PB GCP sing 89 n n 
C3B H3B1 GCP sing 90 n n 
C3B H3B2 GCP sing 91 n n 
PB O1B GCP doub 92 n n 
PB O2B GCP sing 93 n n 
PB O3A GCP sing 94 n n 
O2B HOB2 GCP sing 95 n n 
O3A PA GCP sing 96 n n 
PA O1A GCP doub 97 n n 
PA O2A GCP sing 98 n n 
PA O5' GCP sing 99 n n 
O2A HOA2 GCP sing 100 n n 
O5' C5' GCP sing 101 n n 
C5' C4' GCP sing 102 n n 
C5' "H5'2" GCP sing 103 n n 
C5' "H5'1" GCP sing 104 n n 
C4' O4' GCP sing 105 n n 
C4' C3' GCP sing 106 n n 
C4' H4' GCP sing 107 n n 
O4' C1' GCP sing 108 n n 
C3' O3' GCP sing 109 n n 
C3' C2' GCP sing 110 n n 
C3' H3' GCP sing 111 n n 
O3' HO3' GCP sing 112 n n 
C2' O2' GCP sing 113 n n 
C2' C1' GCP sing 114 n n 
C2' H2' GCP sing 115 n n 
O2' HO2' GCP sing 116 n n 
C1' N9 GCP sing 117 n n 
C1' H1' GCP sing 118 n n 
N9 C8 GCP sing 119 n y 
N9 C4 GCP sing 120 n y 
C8 N7 GCP doub 121 n y 
C8 H8 GCP sing 122 n n 
N7 C5 GCP sing 123 n y 
C5 C6 GCP sing 124 n y 
C5 C4 GCP doub 125 n y 
C6 O6 GCP doub 126 n n 
C6 N1 GCP sing 127 n y 
N1 C2 GCP sing 128 n y 
N1 HN1 GCP sing 129 n n 
C2 N2 GCP sing 130 n n 
C2 N3 GCP doub 131 n y 
N2 HN21 GCP sing 132 n n 
N2 HN22 GCP sing 133 n n 
N3 C4 GCP sing 134 n y 
#
_atom_sites.entry_id                     7SD0 
_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 4 GCP B 1 500 500 GCP GCP . 
E 5 MG B 1 501 501 MG MG . 
F 6 MN C 1 400 400 MN MN . 
G 6 MN C 1 401 401 MN MN . 
#
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 GCP . . . D 4 112.441 92.517 96.343 1 124.29 ? PG GCP 500 B 1 
HETATM 2 O O1G GCP . . . D 4 111.38 93.101 97.191 1 124.29 ? O1G GCP 500 B 1 
HETATM 3 O O2G GCP . . . D 4 112.735 93.448 95.066 1 124.29 ? O2G GCP 500 B 1 
HETATM 4 O O3G GCP . . . D 4 111.958 91.092 95.778 1 124.29 ? O3G GCP 500 B 1 
HETATM 5 C C3B GCP . . . D 4 113.975 92.305 97.281 1 124.29 ? C3B GCP 500 B 1 
HETATM 6 P PB GCP . . . D 4 113.977 92.986 98.964 1 124.29 ? PB GCP 500 B 1 
HETATM 7 O O1B GCP . . . D 4 115.213 92.543 99.643 1 124.29 ? O1B GCP 500 B 1 
HETATM 8 O O2B GCP . . . D 4 113.995 94.59 98.914 1 124.29 ? O2B GCP 500 B 1 
HETATM 9 O O3A GCP . . . D 4 112.715 92.475 99.817 1 124.29 ? O3A GCP 500 B 1 
HETATM 10 P PA GCP . . . D 4 111.953 93.472 100.825 1 124.29 ? PA GCP 500 B 1 
HETATM 11 O O1A GCP . . . D 4 110.749 94.038 100.11 1 124.29 ? O1A GCP 500 B 1 
HETATM 12 O O2A GCP . . . D 4 112.964 94.392 101.464 1 124.29 ? O2A GCP 500 B 1 
HETATM 13 O O5' GCP . . . D 4 111.422 92.48 101.97 1 124.29 ? O5' GCP 500 B 1 
HETATM 14 C C5' GCP . . . D 4 110.501 92.96 102.942 1 124.29 ? C5' GCP 500 B 1 
HETATM 15 C C4' GCP . . . D 4 110.516 92.012 104.129 1 124.29 ? C4' GCP 500 B 1 
HETATM 16 O O4' GCP . . . D 4 111.841 91.884 104.652 1 124.29 ? O4' GCP 500 B 1 
HETATM 17 C C3' GCP . . . D 4 109.632 92.525 105.251 1 124.29 ? C3' GCP 500 B 1 
HETATM 18 O O3' GCP . . . D 4 108.481 91.688 105.376 1 124.29 ? O3' GCP 500 B 1 
HETATM 19 C C2' GCP . . . D 4 110.477 92.446 106.505 1 124.29 ? C2' GCP 500 B 1 
HETATM 20 O O2' GCP . . . D 4 109.837 91.622 107.482 1 124.29 ? O2' GCP 500 B 1 
HETATM 21 C C1' GCP . . . D 4 111.8 91.829 106.079 1 124.29 ? C1' GCP 500 B 1 
HETATM 22 N N9 GCP . . . D 4 112.943 92.576 106.664 1 124.29 ? N9 GCP 500 B 1 
HETATM 23 C C8 GCP . . . D 4 113.7 93.481 106.018 1 124.29 ? C8 GCP 500 B 1 
HETATM 24 N N7 GCP . . . D 4 114.667 93.986 106.825 1 124.29 ? N7 GCP 500 B 1 
HETATM 25 C C5 GCP . . . D 4 114.537 93.391 108.023 1 124.29 ? C5 GCP 500 B 1 
HETATM 26 C C6 GCP . . . D 4 115.232 93.458 109.329 1 124.29 ? C6 GCP 500 B 1 
HETATM 27 O O6 GCP . . . D 4 116.205 94.218 109.501 1 124.29 ? O6 GCP 500 B 1 
HETATM 28 N N1 GCP . . . D 4 114.792 92.677 110.319 1 124.29 ? N1 GCP 500 B 1 
HETATM 29 C C2 GCP . . . D 4 113.748 91.845 110.161 1 124.29 ? C2 GCP 500 B 1 
HETATM 30 N N2 GCP . . . D 4 113.366 91.089 111.215 1 124.29 ? N2 GCP 500 B 1 
HETATM 31 N N3 GCP . . . D 4 113.062 91.728 108.996 1 124.29 ? N3 GCP 500 B 1 
HETATM 32 C C4 GCP . . . D 4 113.403 92.462 107.912 1 124.29 ? C4 GCP 500 B 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           392 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           32 
#