data_7JKR # _model_server_result.job_id kCGUSo5sz6pnBIPo0_gc4g _model_server_result.datetime_utc '2025-07-05 07:40:05' _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 7jkr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 7JKR # _exptl.entry_id 7JKR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 120 _cell.entry_id 7JKR _cell.length_a 99.328 _cell.length_b 99.328 _cell.length_c 134.029 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JKR _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 x,y,z _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 covale ? covale1 B C ASN 331 B ASN 331 1_555 B N CME 332 B CME 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 B C CME 332 B CME 332 1_555 B N ALA 333 B ALA 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 B O ASN 206 B ASN 206 1_555 E MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc2 B OD2 ASP 220 B ASP 220 1_555 E MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc3 D O2G GNP . B GNP 601 1_555 E MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc4 D O3A GNP . B GNP 601 1_555 E MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc5 D O2A GNP . B GNP 601 1_555 E MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? # _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 150 n n PG O2G GNP sing 151 n n PG O3G GNP sing 152 n n PG N3B GNP sing 153 n n O2G HOG2 GNP sing 154 n n O3G HOG3 GNP sing 155 n n N3B PB GNP sing 156 n n N3B HNB3 GNP sing 157 n n PB O1B GNP doub 158 n n PB O2B GNP sing 159 n n PB O3A GNP sing 160 n n O2B HOB2 GNP sing 161 n n O3A PA GNP sing 162 n n PA O1A GNP doub 163 n n PA O2A GNP sing 164 n n PA O5' GNP sing 165 n n O2A HOA2 GNP sing 166 n n O5' C5' GNP sing 167 n n C5' C4' GNP sing 168 n n C5' "H5'2" GNP sing 169 n n C5' "H5'1" GNP sing 170 n n C4' O4' GNP sing 171 n n C4' C3' GNP sing 172 n n C4' H4' GNP sing 173 n n O4' C1' GNP sing 174 n n C3' O3' GNP sing 175 n n C3' C2' GNP sing 176 n n C3' H3' GNP sing 177 n n O3' HO3' GNP sing 178 n n C2' O2' GNP sing 179 n n C2' C1' GNP sing 180 n n C2' H2' GNP sing 181 n n O2' HO2' GNP sing 182 n n C1' N9 GNP sing 183 n n C1' H1' GNP sing 184 n n N9 C8 GNP sing 185 n y N9 C4 GNP sing 186 n y C8 N7 GNP doub 187 n y C8 H8 GNP sing 188 n n N7 C5 GNP sing 189 n y C5 C6 GNP sing 190 n y C5 C4 GNP doub 191 n y C6 O6 GNP doub 192 n n C6 N1 GNP sing 193 n y N1 C2 GNP sing 194 n y N1 HN1 GNP sing 195 n n C2 N2 GNP sing 196 n n C2 N3 GNP doub 197 n y N2 HN21 GNP sing 198 n n N2 HN22 GNP sing 199 n n N3 C4 GNP sing 200 n y # _atom_sites.entry_id 7JKR _atom_sites.fract_transf_matrix[1][1] 0.010068 _atom_sites.fract_transf_matrix[1][2] 0.005813 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011625 _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] 0.007461 _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 GOL A 1 401 401 GOL GOL . D 4 GNP B 1 601 601 GNP GNP . E 5 MG B 1 602 1 MG MG . F 6 HOH A 1 501 7 HOH HOH . F 6 HOH A 2 502 4 HOH HOH . F 6 HOH A 3 503 2 HOH HOH . G 6 HOH B 1 701 1 HOH HOH . G 6 HOH B 2 702 6 HOH HOH . G 6 HOH B 3 703 3 HOH HOH . G 6 HOH B 4 704 5 HOH HOH . # 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 . . . D 4 1.872 36.846 32.501 1 97.48 ? PG GNP 601 B 1 HETATM 2 O O1G GNP . . . D 4 1.878 38.212 31.992 1 101.93 ? O1G GNP 601 B 1 HETATM 3 O O2G GNP . . . D 4 3.212 36.085 32.132 1 96.46 ? O2G GNP 601 B 1 HETATM 4 O O3G GNP . . . D 4 0.671 35.984 31.918 1 110.72 ? O3G GNP 601 B 1 HETATM 5 N N3B GNP . . . D 4 1.729 36.839 34.128 1 108.24 ? N3B GNP 601 B 1 HETATM 6 P PB GNP . . . D 4 1.775 35.593 35.181 1 106.34 ? PB GNP 601 B 1 HETATM 7 O O1B GNP . . . D 4 1.308 35.974 36.509 1 111.13 ? O1B GNP 601 B 1 HETATM 8 O O2B GNP . . . D 4 0.827 34.446 34.624 1 104.66 ? O2B GNP 601 B 1 HETATM 9 O O3A GNP . . . D 4 3.256 34.997 35.191 1 102.47 ? O3A GNP 601 B 1 HETATM 10 P PA GNP . . . D 4 4.33 34.613 36.302 1 98.17 ? PA GNP 601 B 1 HETATM 11 O O1A GNP . . . D 4 4.153 33.22 36.761 1 103.19 ? O1A GNP 601 B 1 HETATM 12 O O2A GNP . . . D 4 5.691 34.893 35.692 1 97.38 ? O2A GNP 601 B 1 HETATM 13 O O5' GNP . . . D 4 4.182 35.663 37.526 1 103.04 ? O5' GNP 601 B 1 HETATM 14 C C5' GNP . . . D 4 4.101 37.082 37.267 1 102.73 ? C5' GNP 601 B 1 HETATM 15 C C4' GNP . . . D 4 5.09 37.816 38.135 1 99.52 ? C4' GNP 601 B 1 HETATM 16 O O4' GNP . . . D 4 5.4 37.036 39.307 1 101.62 ? O4' GNP 601 B 1 HETATM 17 C C3' GNP . . . D 4 6.445 38.101 37.507 1 96.02 ? C3' GNP 601 B 1 HETATM 18 O O3' GNP . . . D 4 6.389 39.257 36.675 1 94.98 ? O3' GNP 601 B 1 HETATM 19 C C2' GNP . . . D 4 7.325 38.328 38.738 1 94.6 ? C2' GNP 601 B 1 HETATM 20 O O2' GNP . . . D 4 7.258 39.679 39.184 1 95.29 ? O2' GNP 601 B 1 HETATM 21 C C1' GNP . . . D 4 6.691 37.39 39.778 1 95.67 ? C1' GNP 601 B 1 HETATM 22 N N9 GNP . . . D 4 7.465 36.156 39.991 1 96.96 ? N9 GNP 601 B 1 HETATM 23 C C8 GNP . . . D 4 7.241 34.857 39.444 1 100.31 ? C8 GNP 601 B 1 HETATM 24 N N7 GNP . . . D 4 8.137 33.955 39.811 1 102.17 ? N7 GNP 601 B 1 HETATM 25 C C5 GNP . . . D 4 9.078 34.558 40.655 1 102.61 ? C5 GNP 601 B 1 HETATM 26 C C6 GNP . . . D 4 10.264 34.181 41.358 1 105.03 ? C6 GNP 601 B 1 HETATM 27 O O6 GNP . . . D 4 10.743 33.047 41.339 1 102.56 ? O6 GNP 601 B 1 HETATM 28 N N1 GNP . . . D 4 10.834 35.17 42.048 1 106.83 ? N1 GNP 601 B 1 HETATM 29 C C2 GNP . . . D 4 10.377 36.475 42.128 1 102.98 ? C2 GNP 601 B 1 HETATM 30 N N2 GNP . . . D 4 11.1 37.308 42.875 1 104.12 ? N2 GNP 601 B 1 HETATM 31 N N3 GNP . . . D 4 9.281 36.934 41.509 1 101.52 ? N3 GNP 601 B 1 HETATM 32 C C4 GNP . . . D 4 8.663 35.988 40.794 1 99.28 ? C4 GNP 601 B 1 HETATM 33 H HOG2 GNP . . . D 4 3.418 35.92 31.175 1 116.26 ? HOG2 GNP 601 B 1 HETATM 34 H HOG3 GNP . . . D 4 0.368 36.143 30.986 1 133.38 ? HOG3 GNP 601 B 1 HETATM 35 H HNB3 GNP . . . D 4 1.591 37.762 34.529 1 130.4 ? HNB3 GNP 601 B 1 HETATM 36 H HOB2 GNP . . . D 4 0.114 34.628 33.958 1 126.1 ? HOB2 GNP 601 B 1 HETATM 37 H HOA2 GNP . . . D 4 6.598 34.659 36.023 1 117.36 ? HOA2 GNP 601 B 1 HETATM 38 H "H5'2" GNP . . . D 4 3.091 37.438 37.465 1 123.78 ? "H5'2" GNP 601 B 1 HETATM 39 H "H5'1" GNP . . . D 4 4.304 37.279 36.216 1 123.78 ? "H5'1" GNP 601 B 1 HETATM 40 H H4' GNP . . . D 4 4.637 38.725 38.529 1 119.93 ? H4' GNP 601 B 1 HETATM 41 H H3' GNP . . . D 4 6.802 37.262 36.912 1 115.73 ? H3' GNP 601 B 1 HETATM 42 H HO3' GNP . . . D 4 7.062 39.129 35.956 1 114.48 ? HO3' GNP 601 B 1 HETATM 43 H H2' GNP . . . D 4 8.358 38.058 38.522 1 114.03 ? H2' GNP 601 B 1 HETATM 44 H HO2' GNP . . . D 4 8.185 40.034 39.169 1 113.05 ? HO2' GNP 601 B 1 HETATM 45 H H1' GNP . . . D 4 6.553 37.883 40.74 1 115.32 ? H1' GNP 601 B 1 HETATM 46 H H8 GNP . . . D 4 6.404 34.636 38.784 1 120.88 ? H8 GNP 601 B 1 HETATM 47 H HN1 GNP . . . D 4 11.677 34.907 42.549 1 128.7 ? HN1 GNP 601 B 1 HETATM 48 H HN21 GNP . . . D 4 10.821 38.278 42.976 1 122.39 ? HN21 GNP 601 B 1 HETATM 49 H HN22 GNP . . . D 4 11.934 36.977 43.349 1 122.39 ? HN22 GNP 601 B 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 49 #