data_6DPU
#
_model_server_result.job_id            Sn6wIlGNMnGhrg35akvgEA 
_model_server_result.datetime_utc      '2025-02-27 17:39:23' 
_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          6dpu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"CA","auth_seq_id":501}' 
#
_entry.id    6DPU 
#
_exptl.entry_id    6DPU 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              521.208 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER' 
_entity.pdbx_number_of_molecules    6 
_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            6DPU 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DPU 
_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    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA 
_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
? 5 O N N 
? 5 S N N 
? 5 W N N 
? 5 Y N N 
? 5 AA N N 
? 5 CA 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 M O3G GTP . A GTP 501 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc2 M O1B GTP . A GTP 501 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc3 O O2G G2P . B G2P 501 1_555 P MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc4 O O2B G2P . B G2P 501 1_555 P MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc5 Q O3G GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc6 Q O1B GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc7 S O2G G2P . D G2P 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc8 S O2B G2P . D G2P 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc9 U O3G GTP . E GTP 501 1_555 V MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc10 U O1B GTP . E GTP 501 1_555 V MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? 
metalc ? metalc11 W O2G G2P . F G2P 501 1_555 X MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc12 W O2B G2P . F G2P 501 1_555 X MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc13 Y O2G G2P . G G2P 501 1_555 Z MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc14 Y O2B G2P . G G2P 501 1_555 Z MG MG . G MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc15 AA O2G G2P . H G2P 501 1_555 BA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc16 AA O2B G2P . H G2P 501 1_555 BA MG MG . H MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc17 CA O2G G2P . I G2P 501 1_555 DA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc18 CA O2B G2P . I G2P 501 1_555 DA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc19 EA O3G GTP . J GTP 501 1_555 FA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? 
metalc ? metalc20 EA O1B GTP . J GTP 501 1_555 FA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? 
metalc ? metalc21 GA O3G GTP . K GTP 501 1_555 HA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc22 GA O1B GTP . K GTP 501 1_555 HA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc23 IA O3G GTP . L GTP 501 1_555 JA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc24 IA O1B GTP . L GTP 501 1_555 JA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
#
_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                     6DPU 
_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
M 3 GTP A 1 501 501 GTP GTP . 
N 4 MG A 1 502 502 MG MG . 
O 5 G2P B 1 501 501 G2P G2P . 
P 4 MG B 1 502 502 MG MG . 
Q 3 GTP C 1 501 501 GTP GTP . 
R 4 MG C 1 502 502 MG MG . 
S 5 G2P D 1 501 501 G2P G2P . 
T 4 MG D 1 502 502 MG MG . 
U 3 GTP E 1 501 501 GTP GTP . 
V 4 MG E 1 502 502 MG MG . 
W 5 G2P F 1 501 501 G2P G2P . 
X 4 MG F 1 502 502 MG MG . 
Y 5 G2P G 1 501 501 G2P G2P . 
Z 4 MG G 1 502 502 MG MG . 
AA 5 G2P H 1 501 501 G2P G2P . 
BA 4 MG H 1 502 502 MG MG . 
CA 5 G2P I 1 501 501 G2P G2P . 
DA 4 MG I 1 502 502 MG MG . 
EA 3 GTP J 1 501 501 GTP GTP . 
FA 4 MG J 1 502 502 MG MG . 
GA 3 GTP K 1 501 501 GTP GTP . 
HA 4 MG K 1 502 502 MG MG . 
IA 3 GTP L 1 501 501 GTP GTP . 
JA 4 MG L 1 502 502 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 G2P . . . CA 5 330.123 389.935 173.394 1 26.45 ? PG G2P 501 I 1 
HETATM 2 O O1G G2P . . . CA 5 328.806 390.565 173.011 1 26.58 ? O1G G2P 501 I 1 
HETATM 3 O O2G G2P . . . CA 5 330.273 388.507 172.917 1 26.44 ? O2G G2P 501 I 1 
HETATM 4 O O3G G2P . . . CA 5 331.335 390.79 173.14 1 26.44 ? O3G G2P 501 I 1 
HETATM 5 O O3B G2P . . . CA 5 330.064 389.904 175.005 1 25.9 ? O3B G2P 501 I 1 
HETATM 6 P PB G2P . . . CA 5 330.348 388.565 175.845 1 25.48 ? PB G2P 501 I 1 
HETATM 7 O O1B G2P . . . CA 5 330.141 388.874 177.274 1 25.49 ? O1B G2P 501 I 1 
HETATM 8 O O2B G2P . . . CA 5 329.488 387.385 175.162 1 25.47 ? O2B G2P 501 I 1 
HETATM 9 C C3A G2P . . . CA 5 332.11 388.234 175.629 1 25.14 ? C3A G2P 501 I 1 
HETATM 10 P PA G2P . . . CA 5 332.506 386.578 176.229 1 24.74 ? PA G2P 501 I 1 
HETATM 11 O O1A G2P . . . CA 5 331.844 386.38 177.539 1 24.74 ? O1A G2P 501 I 1 
HETATM 12 O O2A G2P . . . CA 5 331.935 385.42 175.268 1 24.6 ? O2A G2P 501 I 1 
HETATM 13 O O5' G2P . . . CA 5 334.084 386.496 176.514 1 24.07 ? O5' G2P 501 I 1 
HETATM 14 C C5' G2P . . . CA 5 335.078 385.844 175.725 1 23.75 ? C5' G2P 501 I 1 
HETATM 15 C C4' G2P . . . CA 5 336.24 385.81 176.713 1 23.3 ? C4' G2P 501 I 1 
HETATM 16 O O4' G2P . . . CA 5 335.943 385.062 177.898 1 22.65 ? O4' G2P 501 I 1 
HETATM 17 C C3' G2P . . . CA 5 337.433 384.969 176.274 1 23.05 ? C3' G2P 501 I 1 
HETATM 18 O O3' G2P . . . CA 5 338.653 385.273 176.973 1 23.12 ? O3' G2P 501 I 1 
HETATM 19 C C2' G2P . . . CA 5 336.904 383.551 176.436 1 22.64 ? C2' G2P 501 I 1 
HETATM 20 O O2' G2P . . . CA 5 338.06 382.769 176.143 1 22.94 ? O2' G2P 501 I 1 
HETATM 21 C C1' G2P . . . CA 5 336.408 383.697 177.874 1 22.24 ? C1' G2P 501 I 1 
HETATM 22 N N9 G2P . . . CA 5 335.28 382.757 178.119 1 21.32 ? N9 G2P 501 I 1 
HETATM 23 C C8 G2P . . . CA 5 334.17 382.562 177.374 1 20.99 ? C8 G2P 501 I 1 
HETATM 24 N N7 G2P . . . CA 5 333.368 381.618 177.929 1 20.62 ? N7 G2P 501 I 1 
HETATM 25 C C5 G2P . . . CA 5 333.951 381.204 179.061 1 20.38 ? C5 G2P 501 I 1 
HETATM 26 C C6 G2P . . . CA 5 333.636 380.232 180.132 1 20.09 ? C6 G2P 501 I 1 
HETATM 27 O O6 G2P . . . CA 5 332.591 379.556 180.092 1 19.86 ? O6 G2P 501 I 1 
HETATM 28 N N1 G2P . . . CA 5 334.518 380.081 181.131 1 20.19 ? N1 G2P 501 I 1 
HETATM 29 C C2 G2P . . . CA 5 335.661 380.794 181.202 1 20.35 ? C2 G2P 501 I 1 
HETATM 30 N N2 G2P . . . CA 5 336.492 380.579 182.252 1 20.36 ? N2 G2P 501 I 1 
HETATM 31 N N3 G2P . . . CA 5 336.014 381.707 180.252 1 20.54 ? N3 G2P 501 I 1 
HETATM 32 C C4 G2P . . . CA 5 335.215 381.947 179.178 1 20.75 ? C4 G2P 501 I 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    65 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           32 
#