data_7DMZ
#
_model_server_result.job_id            AKz7xpsT4drDRGyGINu1hQ 
_model_server_result.datetime_utc      '2024-11-10 01:22:15' 
_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          7dmz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":502}' 
#
_entry.id    7DMZ 
#
_exptl.entry_id    7DMZ 
_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    3 
_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            7DMZ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DMZ 
_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    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,H,I,J,K,L,M,N,O,P,Q 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 6 M N N 
? 6 O N N 
? 6 Q N 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 H O2G GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc2 H O3G GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc3 H O1B GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc4 J O2G GTP . B GTP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc5 J O3G GTP . B GTP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.97 ? 
metalc ? metalc6 J O3B GTP . B GTP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc7 J O1B GTP . B GTP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
#
_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                     7DMZ 
_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
G 3 GTP D 1 501 501 GTP GTP . 
H 3 GTP A 1 501 501 GTP GTP . 
I 4 MG A 1 502 502 MG MG . 
J 3 GTP B 1 501 501 GTP GTP . 
K 4 MG B 1 502 502 MG MG . 
L 5 TAJ E 1 501 501 TAJ TAJ . 
M 6 G2P E 1 502 501 G2P G2P . 
N 5 TAJ C 1 501 501 TAJ TAJ . 
O 6 G2P C 1 502 501 G2P G2P . 
P 5 TAJ F 1 501 501 TAJ TAJ . 
Q 6 G2P F 1 502 501 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 . . . Q 6 136.85 108.919 91.726 1 60.11 ? PG G2P 502 F 1 
HETATM 2 O O1G G2P . . . Q 6 138.221 109.301 91.225 1 60.11 ? O1G G2P 502 F 1 
HETATM 3 O O2G G2P . . . Q 6 136.554 107.449 91.563 1 60.11 ? O2G G2P 502 F 1 
HETATM 4 O O3G G2P . . . Q 6 136.581 109.412 93.125 1 60.11 ? O3G G2P 502 F 1 
HETATM 5 O O3B G2P . . . Q 6 135.803 109.701 90.772 1 60.11 ? O3B G2P 502 F 1 
HETATM 6 P PB G2P . . . Q 6 134.217 109.715 90.836 1 60.11 ? PB G2P 502 F 1 
HETATM 7 O O1B G2P . . . Q 6 133.72 108.299 90.78 1 60.11 ? O1B G2P 502 F 1 
HETATM 8 O O2B G2P . . . Q 6 133.796 110.509 92.04 1 60.11 ? O2B G2P 502 F 1 
HETATM 9 C C3A G2P . . . Q 6 133.525 110.554 89.385 1 60.11 ? C3A G2P 502 F 1 
HETATM 10 P PA G2P . . . Q 6 131.823 109.932 89.266 1 60.11 ? PA G2P 502 F 1 
HETATM 11 O O1A G2P . . . Q 6 131.788 108.869 88.205 1 60.11 ? O1A G2P 502 F 1 
HETATM 12 O O2A G2P . . . Q 6 131.456 109.472 90.648 1 60.11 ? O2A G2P 502 F 1 
HETATM 13 O O5' G2P . . . Q 6 130.865 111.141 88.908 1 60.11 ? O5' G2P 502 F 1 
HETATM 14 C C5' G2P . . . Q 6 129.441 111.087 89.177 1 60.11 ? C5' G2P 502 F 1 
HETATM 15 C C4' G2P . . . Q 6 128.732 110.289 88.111 1 60.11 ? C4' G2P 502 F 1 
HETATM 16 O O4' G2P . . . Q 6 129.242 108.938 88.02 1 60.11 ? O4' G2P 502 F 1 
HETATM 17 C C3' G2P . . . Q 6 127.212 110.12 88.263 1 60.11 ? C3' G2P 502 F 1 
HETATM 18 O O3' G2P . . . Q 6 126.531 111.061 87.443 1 60.11 ? O3' G2P 502 F 1 
HETATM 19 C C2' G2P . . . Q 6 126.963 108.656 87.868 1 60.11 ? C2' G2P 502 F 1 
HETATM 20 O O2' G2P . . . Q 6 125.839 108.467 87.036 1 60.11 ? O2' G2P 502 F 1 
HETATM 21 C C1' G2P . . . Q 6 128.295 108.244 87.249 1 60.11 ? C1' G2P 502 F 1 
HETATM 22 N N9 G2P . . . Q 6 128.561 106.812 87.315 1 60.11 ? N9 G2P 502 F 1 
HETATM 23 C C8 G2P . . . Q 6 129.03 106.11 88.395 1 60.11 ? C8 G2P 502 F 1 
HETATM 24 N N7 G2P . . . Q 6 129.169 104.828 88.159 1 60.11 ? N7 G2P 502 F 1 
HETATM 25 C C5 G2P . . . Q 6 128.765 104.672 86.84 1 60.11 ? C5 G2P 502 F 1 
HETATM 26 C C6 G2P . . . Q 6 128.704 103.502 86.038 1 60.11 ? C6 G2P 502 F 1 
HETATM 27 O O6 G2P . . . Q 6 128.995 102.341 86.356 1 60.11 ? O6 G2P 502 F 1 
HETATM 28 N N1 G2P . . . Q 6 128.234 103.782 84.754 1 60.11 ? N1 G2P 502 F 1 
HETATM 29 C C2 G2P . . . Q 6 127.88 105.033 84.307 1 60.11 ? C2 G2P 502 F 1 
HETATM 30 N N2 G2P . . . Q 6 127.452 105.114 83.04 1 60.11 ? N2 G2P 502 F 1 
HETATM 31 N N3 G2P . . . Q 6 127.94 106.136 85.056 1 60.11 ? N3 G2P 502 F 1 
HETATM 32 C C4 G2P . . . Q 6 128.389 105.887 86.31 1 60.11 ? C4 G2P 502 F 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    50 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           32 
#