data_7D9S
#
_model_server_result.job_id            tSeUSkVgEQy5qW5UXYp3NA 
_model_server_result.datetime_utc      '2024-12-23 00:32:09' 
_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          7d9s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":703}' 
#
_entry.id    7D9S 
#
_exptl.entry_id    7D9S 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              521.208 
_entity.id                          6 
_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            7D9S 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7D9S 
_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,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                      6 
_struct_asym.id                             G 
_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 OD1 ASP 486 A ASP 486 1_555 C MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc2 A OD1 ASP 486 A ASP 486 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc3 A OD2 ASP 486 A ASP 486 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc4 A O ILE 487 A ILE 487 1_555 D MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
metalc ? metalc5 A OD2 ASP 530 A ASP 530 1_555 C MG MG . A MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc6 C MG MG . A MG 701 1_555 G O5' G2P . B G2P 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? 
metalc ? metalc7 C MG MG . A MG 701 1_555 G O3B G2P . B G2P 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? 
metalc ? metalc8 D MG MG . A MG 702 1_555 G O1G G2P . B G2P 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc9 D MG MG . A MG 702 1_555 G O3B G2P . B G2P 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc10 D MG MG . A MG 702 1_555 G O2B G2P . B G2P 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
#
_chem_comp.formula           'C11 H18 N5 O13 P3' 
_chem_comp.formula_weight    521.208 
_chem_comp.id                G2P 
_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 G2P sing 83 n n 
PG O2G G2P doub 84 n n 
PG O3G G2P sing 85 n n 
PG O3B G2P sing 86 n n 
O3B PB G2P sing 87 n n 
PB O1B G2P sing 88 n n 
PB O2B G2P doub 89 n n 
PB C3A G2P sing 90 n n 
C3A PA G2P sing 91 n n 
C3A H3A1 G2P sing 92 n n 
C3A H3A2 G2P sing 93 n n 
PA O1A G2P sing 94 n n 
PA O2A G2P doub 95 n n 
PA O5' G2P sing 96 n n 
O5' C5' G2P sing 97 n n 
C5' C4' G2P sing 98 n n 
C5' "H5'1" G2P sing 99 n n 
C5' "H5'2" G2P sing 100 n n 
C4' O4' G2P sing 101 n n 
C4' C3' G2P sing 102 n n 
C4' H4' G2P sing 103 n n 
O4' C1' G2P sing 104 n n 
C3' O3' G2P sing 105 n n 
C3' C2' G2P sing 106 n n 
C3' H3' G2P sing 107 n n 
O3' HA G2P sing 108 n n 
C2' O2' G2P sing 109 n n 
C2' C1' G2P sing 110 n n 
C2' H2' G2P sing 111 n n 
O2' HB G2P sing 112 n n 
C1' N9 G2P sing 113 n n 
C1' H1' G2P sing 114 n n 
N9 C8 G2P sing 115 n y 
N9 C4 G2P sing 116 n y 
C8 N7 G2P doub 117 n y 
C8 H8 G2P sing 118 n n 
N7 C5 G2P sing 119 n y 
C5 C6 G2P sing 120 n y 
C5 C4 G2P doub 121 n y 
C6 O6 G2P doub 122 n n 
C6 N1 G2P sing 123 n y 
N1 C2 G2P sing 124 n y 
N1 H1 G2P sing 125 n n 
C2 N2 G2P sing 126 n n 
C2 N3 G2P doub 127 n y 
N2 H2N1 G2P sing 128 n n 
N2 H2N2 G2P sing 129 n n 
N3 C4 G2P sing 130 n y 
HO1 O1G G2P sing 131 n n 
HO2 O3G G2P sing 132 n n 
HO3 O1A G2P sing 133 n n 
HO4 O1B G2P sing 134 n n 
#
_atom_sites.entry_id                     7D9S 
_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 MG A 1 701 1002 MG MG . 
D 3 MG A 1 702 1101 MG MG . 
E 4 YC1 B 1 701 1002 YC1 YC1 . 
F 5 HEM B 1 702 1000 HEM HEM . 
G 6 G2P B 1 703 1001 G2P G2P . 
#
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 G2P . . . G 6 185.694 128.668 127.919 1 118.07 ? PG G2P 703 B 1 
HETATM 2 O O1G G2P . . . G 6 185.686 129.015 129.387 1 118.07 ? O1G G2P 703 B 1 
HETATM 3 O O2G G2P . . . G 6 185.402 129.827 126.998 1 118.07 ? O2G G2P 703 B 1 
HETATM 4 O O3G G2P . . . G 6 186.854 127.804 127.49 1 118.07 ? O3G G2P 703 B 1 
HETATM 5 O O3B G2P . . . G 6 184.423 127.703 127.742 1 118.07 ? O3B G2P 703 B 1 
HETATM 6 P PB G2P . . . G 6 184.456 126.266 128.454 1 118.07 ? PB G2P 703 B 1 
HETATM 7 O O1B G2P . . . G 6 185.7 125.427 127.874 1 118.07 ? O1B G2P 703 B 1 
HETATM 8 O O2B G2P . . . G 6 184.623 126.447 129.911 1 118.07 ? O2B G2P 703 B 1 
HETATM 9 C C3A G2P . . . G 6 182.922 125.365 128.127 1 118.07 ? C3A G2P 703 B 1 
HETATM 10 P PA G2P . . . G 6 182.629 125.269 126.344 1 118.07 ? PA G2P 703 B 1 
HETATM 11 O O1A G2P . . . G 6 183.552 126.36 125.607 1 118.07 ? O1A G2P 703 B 1 
HETATM 12 O O2A G2P . . . G 6 182.985 123.921 125.852 1 118.07 ? O2A G2P 703 B 1 
HETATM 13 O O5' G2P . . . G 6 181.085 125.568 126.012 1 118.07 ? O5' G2P 703 B 1 
HETATM 14 C C5' G2P . . . G 6 180.219 124.462 125.773 1 118.07 ? C5' G2P 703 B 1 
HETATM 15 C C4' G2P . . . G 6 179.817 124.413 124.308 1 118.07 ? C4' G2P 703 B 1 
HETATM 16 O O4' G2P . . . G 6 178.895 123.338 124.124 1 118.07 ? O4' G2P 703 B 1 
HETATM 17 C C3' G2P . . . G 6 179.122 125.689 123.875 1 118.07 ? C3' G2P 703 B 1 
HETATM 18 O O3' G2P . . . G 6 179.701 126.161 122.656 1 118.07 ? O3' G2P 703 B 1 
HETATM 19 C C2' G2P . . . G 6 177.677 125.31 123.637 1 118.07 ? C2' G2P 703 B 1 
HETATM 20 O O2' G2P . . . G 6 177.226 125.869 122.4 1 118.07 ? O2' G2P 703 B 1 
HETATM 21 C C1' G2P . . . G 6 177.668 123.796 123.555 1 118.07 ? C1' G2P 703 B 1 
HETATM 22 N N9 G2P . . . G 6 176.529 123.235 124.316 1 118.07 ? N9 G2P 703 B 1 
HETATM 23 C C8 G2P . . . G 6 176.581 122.775 125.577 1 118.07 ? C8 G2P 703 B 1 
HETATM 24 N N7 G2P . . . G 6 175.369 122.324 125.983 1 118.07 ? N7 G2P 703 B 1 
HETATM 25 C C5 G2P . . . G 6 174.513 122.495 124.961 1 118.07 ? C5 G2P 703 B 1 
HETATM 26 C C6 G2P . . . G 6 173.077 122.232 124.719 1 118.07 ? C6 G2P 703 B 1 
HETATM 27 O O6 G2P . . . G 6 172.357 121.724 125.604 1 118.07 ? O6 G2P 703 B 1 
HETATM 28 N N1 G2P . . . G 6 172.575 122.555 123.523 1 118.07 ? N1 G2P 703 B 1 
HETATM 29 C C2 G2P . . . G 6 173.329 123.104 122.554 1 118.07 ? C2 G2P 703 B 1 
HETATM 30 N N2 G2P . . . G 6 172.741 123.4 121.372 1 118.07 ? N2 G2P 703 B 1 
HETATM 31 N N3 G2P . . . G 6 174.65 123.372 122.706 1 118.07 ? N3 G2P 703 B 1 
HETATM 32 C C4 G2P . . . G 6 175.284 123.094 123.865 1 118.07 ? C4 G2P 703 B 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           347 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           32 
#