data_6HZ4
#
_model_server_result.job_id            5-62D_ETyPdN1EGl8m8uFw 
_model_server_result.datetime_utc      '2025-03-06 08:49:24' 
_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          6hz4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1001}' 
#
_entry.id    6HZ4 
#
_exptl.entry_id    6HZ4 
_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    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            6HZ4 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6HZ4 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_and_software_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
? 3 I N N 
? 3 K N N 
? 3 M 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 A OG1 THR 47 A THR 208 1_555 J MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc2 A OD2 ASP 118 A ASP 279 1_555 J MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? 
metalc ? metalc3 I O3G GNP . A GNP 1001 1_555 J MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc4 I O1B GNP . A GNP 1001 1_555 J MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc5 B OG1 THR 47 B THR 208 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc6 B OD2 ASP 118 B ASP 279 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? 
metalc ? metalc7 K O3G GNP . B GNP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? 
metalc ? metalc8 K O2B GNP . B GNP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? 
metalc ? metalc9 C OG1 THR 47 C THR 208 1_555 N MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc10 C OD2 ASP 118 C ASP 279 1_555 N MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? 
metalc ? metalc11 M O3G GNP . C GNP 1001 1_555 N MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? 
metalc ? metalc12 M O2B GNP . C GNP 1001 1_555 N MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? 
#
_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 174 n n 
PG O2G GNP sing 175 n n 
PG O3G GNP sing 176 n n 
PG N3B GNP sing 177 n n 
O2G HOG2 GNP sing 178 n n 
O3G HOG3 GNP sing 179 n n 
N3B PB GNP sing 180 n n 
N3B HNB3 GNP sing 181 n n 
PB O1B GNP doub 182 n n 
PB O2B GNP sing 183 n n 
PB O3A GNP sing 184 n n 
O2B HOB2 GNP sing 185 n n 
O3A PA GNP sing 186 n n 
PA O1A GNP doub 187 n n 
PA O2A GNP sing 188 n n 
PA O5' GNP sing 189 n n 
O2A HOA2 GNP sing 190 n n 
O5' C5' GNP sing 191 n n 
C5' C4' GNP sing 192 n n 
C5' "H5'2" GNP sing 193 n n 
C5' "H5'1" GNP sing 194 n n 
C4' O4' GNP sing 195 n n 
C4' C3' GNP sing 196 n n 
C4' H4' GNP sing 197 n n 
O4' C1' GNP sing 198 n n 
C3' O3' GNP sing 199 n n 
C3' C2' GNP sing 200 n n 
C3' H3' GNP sing 201 n n 
O3' HO3' GNP sing 202 n n 
C2' O2' GNP sing 203 n n 
C2' C1' GNP sing 204 n n 
C2' H2' GNP sing 205 n n 
O2' HO2' GNP sing 206 n n 
C1' N9 GNP sing 207 n n 
C1' H1' GNP sing 208 n n 
N9 C8 GNP sing 209 n y 
N9 C4 GNP sing 210 n y 
C8 N7 GNP doub 211 n y 
C8 H8 GNP sing 212 n n 
N7 C5 GNP sing 213 n y 
C5 C6 GNP sing 214 n y 
C5 C4 GNP doub 215 n y 
C6 O6 GNP doub 216 n n 
C6 N1 GNP sing 217 n y 
N1 C2 GNP sing 218 n y 
N1 HN1 GNP sing 219 n n 
C2 N2 GNP sing 220 n n 
C2 N3 GNP doub 221 n y 
N2 HN21 GNP sing 222 n n 
N2 HN22 GNP sing 223 n n 
N3 C4 GNP sing 224 n y 
#
_atom_sites.entry_id                     6HZ4 
_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
I 3 GNP A 1 1001 1001 GNP GNP . 
J 4 MG A 1 1002 1002 MG MG . 
K 3 GNP B 1 1001 1001 GNP GNP . 
L 4 MG B 1 1002 1002 MG MG . 
M 3 GNP C 1 1001 1001 GNP GNP . 
N 4 MG C 1 1002 1002 MG MG . 
O 5 GDP D 1 1001 1001 GDP GDP . 
P 5 GDP E 1 1001 1001 GDP GDP . 
Q 5 GDP F 1 1001 1001 GDP GDP . 
#
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 . . . M 3 63.394 136.458 116.586 1 39.56 ? PG GNP 1001 C 1 
HETATM 2 O O1G GNP . . . M 3 64.344 136.285 115.481 1 39.56 ? O1G GNP 1001 C 1 
HETATM 3 O O2G GNP . . . M 3 64.141 136.676 117.836 1 39.56 ? O2G GNP 1001 C 1 
HETATM 4 O O3G GNP . . . M 3 62.485 135.298 116.68 1 39.56 ? O3G GNP 1001 C 1 
HETATM 5 N N3B GNP . . . M 3 62.595 137.657 116.314 1 39.56 ? N3B GNP 1001 C 1 
HETATM 6 P PB GNP . . . M 3 62.133 137.866 114.959 1 39.56 ? PB GNP 1001 C 1 
HETATM 7 O O1B GNP . . . M 3 63.209 138.464 114.162 1 39.56 ? O1B GNP 1001 C 1 
HETATM 8 O O2B GNP . . . M 3 61.689 136.576 114.419 1 39.56 ? O2B GNP 1001 C 1 
HETATM 9 O O3A GNP . . . M 3 60.917 138.858 115.092 1 39.56 ? O3A GNP 1001 C 1 
HETATM 10 P PA GNP . . . M 3 59.448 138.266 115.052 1 39.56 ? PA GNP 1001 C 1 
HETATM 11 O O1A GNP . . . M 3 59.217 137.631 113.75 1 39.56 ? O1A GNP 1001 C 1 
HETATM 12 O O2A GNP . . . M 3 59.317 137.248 116.105 1 39.56 ? O2A GNP 1001 C 1 
HETATM 13 O O5' GNP . . . M 3 58.368 139.399 115.301 1 39.56 ? O5' GNP 1001 C 1 
HETATM 14 C C5' GNP . . . M 3 58.64 140.079 116.488 1 39.56 ? C5' GNP 1001 C 1 
HETATM 15 C C4' GNP . . . M 3 57.803 141.32 116.865 1 39.56 ? C4' GNP 1001 C 1 
HETATM 16 O O4' GNP . . . M 3 57.885 142.436 115.878 1 39.56 ? O4' GNP 1001 C 1 
HETATM 17 C C3' GNP . . . M 3 56.342 141.07 116.982 1 39.56 ? C3' GNP 1001 C 1 
HETATM 18 O O3' GNP . . . M 3 55.797 142.038 117.857 1 39.56 ? O3' GNP 1001 C 1 
HETATM 19 C C2' GNP . . . M 3 55.901 141.312 115.594 1 39.56 ? C2' GNP 1001 C 1 
HETATM 20 O O2' GNP . . . M 3 54.489 141.434 115.523 1 39.56 ? O2' GNP 1001 C 1 
HETATM 21 C C1' GNP . . . M 3 56.54 142.644 115.354 1 39.56 ? C1' GNP 1001 C 1 
HETATM 22 N N9 GNP . . . M 3 56.402 143.021 113.93 1 39.56 ? N9 GNP 1001 C 1 
HETATM 23 C C8 GNP . . . M 3 57.176 142.854 112.872 1 39.56 ? C8 GNP 1001 C 1 
HETATM 24 N N7 GNP . . . M 3 56.565 143.367 111.816 1 39.56 ? N7 GNP 1001 C 1 
HETATM 25 C C5 GNP . . . M 3 55.394 143.824 112.218 1 39.56 ? C5 GNP 1001 C 1 
HETATM 26 C C6 GNP . . . M 3 54.413 144.412 111.556 1 39.56 ? C6 GNP 1001 C 1 
HETATM 27 O O6 GNP . . . M 3 54.517 144.613 110.352 1 39.56 ? O6 GNP 1001 C 1 
HETATM 28 N N1 GNP . . . M 3 53.258 144.809 112.223 1 39.56 ? N1 GNP 1001 C 1 
HETATM 29 C C2 GNP . . . M 3 53.164 144.575 113.593 1 39.56 ? C2 GNP 1001 C 1 
HETATM 30 N N2 GNP . . . M 3 52.081 144.923 114.295 1 39.56 ? N2 GNP 1001 C 1 
HETATM 31 N N3 GNP . . . M 3 54.194 143.974 114.197 1 39.56 ? N3 GNP 1001 C 1 
HETATM 32 C C4 GNP . . . M 3 55.292 143.611 113.52 1 39.56 ? C4 GNP 1001 C 1 
HETATM 33 H HNB3 GNP . . . M 3 62.396 138.309 117.027 1 39.56 ? HNB3 GNP 1001 C 1 
HETATM 34 H "H5'2" GNP . . . M 3 59.664 140.372 116.453 1 39.56 ? "H5'2" GNP 1001 C 1 
HETATM 35 H "H5'1" GNP . . . M 3 58.524 139.339 117.256 1 39.56 ? "H5'1" GNP 1001 C 1 
HETATM 36 H H4' GNP . . . M 3 58.164 141.604 117.833 1 39.56 ? H4' GNP 1001 C 1 
HETATM 37 H H3' GNP . . . M 3 56.127 140.081 117.355 1 39.56 ? H3' GNP 1001 C 1 
HETATM 38 H HO3' GNP . . . M 3 54.819 141.909 117.906 1 39.56 ? HO3' GNP 1001 C 1 
HETATM 39 H H2' GNP . . . M 3 56.303 140.577 114.936 1 39.56 ? H2' GNP 1001 C 1 
HETATM 40 H HO2' GNP . . . M 3 54.196 142.151 116.139 1 39.56 ? HO2' GNP 1001 C 1 
HETATM 41 H H1' GNP . . . M 3 56.055 143.389 115.944 1 39.56 ? H1' GNP 1001 C 1 
HETATM 42 H H8 GNP . . . M 3 58.158 142.419 112.859 1 39.56 ? H8 GNP 1001 C 1 
HETATM 43 H HN1 GNP . . . M 3 52.519 145.253 111.724 1 39.56 ? HN1 GNP 1001 C 1 
HETATM 44 H HN21 GNP . . . M 3 51.308 145.353 113.835 1 39.56 ? HN21 GNP 1001 C 1 
HETATM 45 H HN22 GNP . . . M 3 52.023 144.747 115.28 1 39.56 ? HN22 GNP 1001 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    47 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           45 
#