data_8T09 # _model_server_result.job_id 1jvbeUQOmn2j1RJOUzI9hA _model_server_result.datetime_utc '2024-11-15 06:46:09' _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 8t09 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 8T09 # _exptl.entry_id 8T09 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 5 _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 91.544 _cell.angle_gamma 90 _cell.entry_id 8T09 _cell.length_a 57.53 _cell.length_b 77.922 _cell.length_c 58.711 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8T09 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 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 5 _struct_asym.id E _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 A NZ LYS 302 A LYS 720 1_555 C C8 XHZ . A XHZ 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? metalc ? metalc1 B OG SER 17 B SER 17 1_555 D MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc2 B OG1 THR 35 B THR 35 1_555 D MG MG . B MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc3 D MG MG . B MG 200 1_555 E O1B GNP . B GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc4 D MG MG . B MG 200 1_555 E O1G GNP . B GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc5 D MG MG . B MG 200 1_555 G O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc6 D MG MG . B MG 200 1_555 G O HOH . B HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? # _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 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 8T09 _atom_sites.fract_transf_matrix[1][1] 0.017382 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000469 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012833 _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] 0.017039 _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 XHZ A 1 801 801 XHZ DRG . D 4 MG B 1 200 200 MG MG . E 5 GNP B 1 201 201 GNP GNP . F 6 HOH A 1 901 44 HOH HOH . F 6 HOH A 2 902 55 HOH HOH . F 6 HOH A 3 903 7 HOH HOH . F 6 HOH A 4 904 10 HOH HOH . F 6 HOH A 5 905 24 HOH HOH . F 6 HOH A 6 906 3 HOH HOH . F 6 HOH A 7 907 15 HOH HOH . F 6 HOH A 8 908 56 HOH HOH . F 6 HOH A 9 909 57 HOH HOH . F 6 HOH A 10 910 1 HOH HOH . F 6 HOH A 11 911 14 HOH HOH . F 6 HOH A 12 912 45 HOH HOH . F 6 HOH A 13 913 9 HOH HOH . F 6 HOH A 14 914 19 HOH HOH . F 6 HOH A 15 915 54 HOH HOH . F 6 HOH A 16 916 6 HOH HOH . F 6 HOH A 17 917 8 HOH HOH . F 6 HOH A 18 918 46 HOH HOH . F 6 HOH A 19 919 13 HOH HOH . F 6 HOH A 20 920 16 HOH HOH . F 6 HOH A 21 921 47 HOH HOH . F 6 HOH A 22 922 11 HOH HOH . F 6 HOH A 23 923 12 HOH HOH . F 6 HOH A 24 924 26 HOH HOH . F 6 HOH A 25 925 23 HOH HOH . F 6 HOH A 26 926 22 HOH HOH . F 6 HOH A 27 927 20 HOH HOH . F 6 HOH A 28 928 5 HOH HOH . F 6 HOH A 29 929 34 HOH HOH . F 6 HOH A 30 930 50 HOH HOH . F 6 HOH A 31 931 25 HOH HOH . F 6 HOH A 32 932 21 HOH HOH . F 6 HOH A 33 933 48 HOH HOH . F 6 HOH A 34 934 51 HOH HOH . G 6 HOH B 1 301 28 HOH HOH . G 6 HOH B 2 302 33 HOH HOH . G 6 HOH B 3 303 30 HOH HOH . G 6 HOH B 4 304 35 HOH HOH . G 6 HOH B 5 305 42 HOH HOH . G 6 HOH B 6 306 37 HOH HOH . G 6 HOH B 7 307 31 HOH HOH . G 6 HOH B 8 308 58 HOH HOH . G 6 HOH B 9 309 2 HOH HOH . G 6 HOH B 10 310 52 HOH HOH . G 6 HOH B 11 311 38 HOH HOH . G 6 HOH B 12 312 32 HOH HOH . G 6 HOH B 13 313 27 HOH HOH . G 6 HOH B 14 314 40 HOH HOH . G 6 HOH B 15 315 36 HOH HOH . G 6 HOH B 16 316 29 HOH HOH . G 6 HOH B 17 317 53 HOH HOH . G 6 HOH B 18 318 43 HOH HOH . G 6 HOH B 19 319 41 HOH HOH . G 6 HOH B 20 320 4 HOH HOH . G 6 HOH B 21 321 39 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 . . . E 5 2.865 7.397 31.006 1 41.01 ? PG GNP 201 B 1 HETATM 2 O O1G GNP . . . E 5 3.328 8.295 29.897 1 38.97 ? O1G GNP 201 B 1 HETATM 3 O O2G GNP . . . E 5 1.71 8.069 31.753 1 35.7 ? O2G GNP 201 B 1 HETATM 4 O O3G GNP . . . E 5 4.048 7.159 31.983 1 45.61 ? O3G GNP 201 B 1 HETATM 5 N N3B GNP . . . E 5 2.352 5.904 30.344 1 38.84 ? N3B GNP 201 B 1 HETATM 6 P PB GNP . . . E 5 1.299 5.831 29.082 1 39.75 ? PB GNP 201 B 1 HETATM 7 O O1B GNP . . . E 5 1.707 6.788 27.987 1 32.15 ? O1B GNP 201 B 1 HETATM 8 O O2B GNP . . . E 5 -0.092 6.183 29.55 1 43.19 ? O2B GNP 201 B 1 HETATM 9 O O3A GNP . . . E 5 1.284 4.302 28.477 1 38.66 ? O3A GNP 201 B 1 HETATM 10 P PA GNP . . . E 5 2.185 3.875 27.238 1 45.07 ? PA GNP 201 B 1 HETATM 11 O O1A GNP . . . E 5 1.47 4.359 25.978 1 46.37 -1 O1A GNP 201 B 1 HETATM 12 O O2A GNP . . . E 5 3.576 4.336 27.417 1 35.38 ? O2A GNP 201 B 1 HETATM 13 O O5' GNP . . . E 5 2.136 2.305 27.284 1 47.09 ? O5' GNP 201 B 1 HETATM 14 C C5' GNP . . . E 5 2.627 1.574 28.427 1 50.1 ? C5' GNP 201 B 1 HETATM 15 C C4' GNP . . . E 5 2.758 0.116 28.063 1 49.65 ? C4' GNP 201 B 1 HETATM 16 O O4' GNP . . . E 5 1.46 -0.414 27.707 1 48.76 ? O4' GNP 201 B 1 HETATM 17 C C3' GNP . . . E 5 3.69 -0.189 26.889 1 46.05 ? C3' GNP 201 B 1 HETATM 18 O O3' GNP . . . E 5 4.48 -1.344 27.147 1 48.82 ? O3' GNP 201 B 1 HETATM 19 C C2' GNP . . . E 5 2.72 -0.404 25.723 1 44.44 ? C2' GNP 201 B 1 HETATM 20 O O2' GNP . . . E 5 3.233 -1.307 24.751 1 46.05 ? O2' GNP 201 B 1 HETATM 21 C C1' GNP . . . E 5 1.525 -1.032 26.437 1 50.25 ? C1' GNP 201 B 1 HETATM 22 N N9 GNP . . . E 5 0.253 -0.796 25.738 1 49.65 ? N9 GNP 201 B 1 HETATM 23 C C8 GNP . . . E 5 -0.299 0.418 25.422 1 46.03 ? C8 GNP 201 B 1 HETATM 24 N N7 GNP . . . E 5 -1.443 0.317 24.785 1 50.95 ? N7 GNP 201 B 1 HETATM 25 C C5 GNP . . . E 5 -1.654 -1.048 24.675 1 49.13 ? C5 GNP 201 B 1 HETATM 26 C C6 GNP . . . E 5 -2.735 -1.797 24.079 1 47.07 ? C6 GNP 201 B 1 HETATM 27 O O6 GNP . . . E 5 -3.734 -1.35 23.52 1 49.55 ? O6 GNP 201 B 1 HETATM 28 N N1 GNP . . . E 5 -2.543 -3.159 24.193 1 51.89 ? N1 GNP 201 B 1 HETATM 29 C C2 GNP . . . E 5 -1.468 -3.757 24.796 1 53.76 ? C2 GNP 201 B 1 HETATM 30 N N2 GNP . . . E 5 -1.453 -5.091 24.817 1 55.21 ? N2 GNP 201 B 1 HETATM 31 N N3 GNP . . . E 5 -0.463 -3.079 25.35 1 53.92 ? N3 GNP 201 B 1 HETATM 32 C C4 GNP . . . E 5 -0.617 -1.745 25.256 1 48.81 ? C4 GNP 201 B 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 392 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #