data_9G85 # _model_server_result.job_id GNVviDzTDP7uKGPzwL4FxA _model_server_result.datetime_utc '2025-08-13 13:46:50' _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 9g85 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":505}' # _entry.id 9G85 # _exptl.entry_id 9G85 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.16 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5',3'-TETRAPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 9G85 _cell.length_a 133.001 _cell.length_b 133.001 _cell.length_c 510.767 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9G85 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,O,P,Q,R,S,T,Y,AA 1 1 B,D,I,J,K,L,M,N,U,V,W,X,Z,BA 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 K N N ? 3 S N N ? 3 W 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 OD1 ASP 10 A ASP 10 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc2 A OD2 ASP 53 A ASP 53 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc3 A O MET 55 A MET 55 1_555 G MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc4 A OD2 ASP 327 A ASP 327 1_555 H MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc5 A O ILE 328 A ILE 328 1_555 H MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc6 A OE1 GLU 370 A GLU 370 1_555 H MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc7 A OE2 GLU 370 A GLU 370 1_555 H MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc8 F O3B G4P . A G4P 502 1_555 H MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.872 ? metalc ? metalc9 F O2A G4P . A G4P 502 1_555 H MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc10 B OD1 ASP 10 B ASP 10 1_555 M MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc11 B OD2 ASP 53 B ASP 53 1_555 M MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc12 B O MET 55 B MET 55 1_555 M MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? metalc ? metalc13 B OD1 ASP 327 B ASP 327 1_555 N MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc14 B O ILE 328 B ILE 328 1_555 N MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc15 K O3A G4P . B G4P 503 1_555 N MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc16 C OD1 ASP 10 C ASP 10 1_555 O MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc17 C OD2 ASP 53 C ASP 53 1_555 O MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc18 C O MET 55 C MET 55 1_555 O MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc19 C OD1 ASP 327 C ASP 327 1_555 T MG MG . C MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc20 C O ILE 328 C ILE 328 1_555 T MG MG . C MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc21 C OE1 GLU 370 C GLU 370 1_555 T MG MG . C MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc22 S O1B G4P . C G4P 505 1_555 T MG MG . C MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc23 S O1A G4P . C G4P 505 1_555 T MG MG . C MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc24 D OD1 ASP 10 D ASP 10 1_555 U MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc25 D OD2 ASP 53 D ASP 53 1_555 U MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc26 D O MET 55 D MET 55 1_555 U MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc27 D OD1 ASP 327 D ASP 327 1_555 X MG MG . D MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc28 D O ILE 328 D ILE 328 1_555 X MG MG . D MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc29 D OE1 GLU 370 D GLU 370 1_555 X MG MG . D MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc30 W O3B G4P . D G4P 503 1_555 X MG MG . D MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc31 W O1A G4P . D G4P 503 1_555 X MG MG . D MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _chem_comp.formula 'C10 H17 N5 O17 P4' _chem_comp.formula_weight 603.16 _chem_comp.id G4P _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5',3'-TETRAPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms 'guanosine tetraphosphate;ppGpp' # 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 PB O1B G4P doub 159 n n PB O2B G4P sing 160 n n PB O3B G4P sing 161 n n PB O3A G4P sing 162 n n O2B HOB2 G4P sing 163 n n O3B HOB3 G4P sing 164 n n O3A PA G4P sing 165 n n PA O1A G4P doub 166 n n PA O2A G4P sing 167 n n PA O5' G4P sing 168 n n O2A HOA2 G4P sing 169 n n O5' C5' G4P sing 170 n n C5' C4' G4P sing 171 n n C5' H5' G4P sing 172 n n C5' "H5''" G4P sing 173 n n C4' O4' G4P sing 174 n n C4' C3' G4P sing 175 n n C4' H4' G4P sing 176 n n O4' C1' G4P sing 177 n n C3' O3' G4P sing 178 n n C3' C2' G4P sing 179 n n C3' H3' G4P sing 180 n n O3' PC G4P sing 181 n n C2' O2' G4P sing 182 n n C2' C1' G4P sing 183 n n C2' H2' G4P sing 184 n n O2' HO2' G4P sing 185 n n C1' N9 G4P sing 186 n n C1' H1' G4P sing 187 n n N9 C8 G4P sing 188 n y N9 C4 G4P sing 189 n y C8 N7 G4P doub 190 n y C8 H8 G4P sing 191 n n N7 C5 G4P sing 192 n y C5 C6 G4P sing 193 n n C5 C4 G4P doub 194 n y C6 O6 G4P doub 195 n n C6 N1 G4P sing 196 n n N1 C2 G4P sing 197 n n N1 HN1 G4P sing 198 n n C2 N2 G4P sing 199 n n C2 N3 G4P doub 200 n n N2 HN21 G4P sing 201 n n N2 HN22 G4P sing 202 n n N3 C4 G4P sing 203 n n PC O1C G4P doub 204 n n PC O2C G4P sing 205 n n PC O3C G4P sing 206 n n O2C H2C G4P sing 207 n n O3C PD G4P sing 208 n n PD O1D G4P doub 209 n n PD O2D G4P sing 210 n n PD O3D G4P sing 211 n n O2D H2D G4P sing 212 n n O3D H3D G4P sing 213 n n # _atom_sites.entry_id 9G85 _atom_sites.fract_transf_matrix[1][1] 0.007519 _atom_sites.fract_transf_matrix[1][2] 0.004341 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008682 _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] 0.001958 _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 E 2 C2E A 1 501 503 C2E C2E . F 3 G4P A 1 502 506 G4P G4P . G 4 MG A 1 503 1 MG MG . H 4 MG A 1 504 7 MG MG . I 2 C2E B 1 501 503 C2E C2E . J 2 C2E B 1 502 505 C2E C2E . K 3 G4P B 1 503 506 G4P G4P . L 2 C2E B 1 504 503 C2E C2E . M 4 MG B 1 505 11 MG MG . N 4 MG B 1 506 13 MG MG . O 4 MG C 1 501 500 MG MG . P 2 C2E C 1 502 505 C2E C2E . Q 2 C2E C 1 503 503 C2E C2E . R 2 C2E C 1 504 505 C2E C2E . S 3 G4P C 1 505 506 G4P G4P . T 4 MG C 1 506 9 MG MG . U 4 MG D 1 501 500 MG MG . V 2 C2E D 1 502 505 C2E C2E . W 3 G4P D 1 503 506 G4P G4P . X 4 MG D 1 504 12 MG MG . Y 5 HOH A 1 601 27 HOH HOH . Y 5 HOH A 2 602 26 HOH HOH . Y 5 HOH A 3 603 24 HOH HOH . Y 5 HOH A 4 604 32 HOH HOH . Y 5 HOH A 5 605 9 HOH HOH . Y 5 HOH A 6 606 1 HOH HOH . Y 5 HOH A 7 607 13 HOH HOH . Z 5 HOH B 1 601 28 HOH HOH . Z 5 HOH B 2 602 17 HOH HOH . Z 5 HOH B 3 603 19 HOH HOH . Z 5 HOH B 4 604 37 HOH HOH . Z 5 HOH B 5 605 23 HOH HOH . Z 5 HOH B 6 606 3 HOH HOH . Z 5 HOH B 7 607 5 HOH HOH . Z 5 HOH B 8 608 33 HOH HOH . Z 5 HOH B 9 609 15 HOH HOH . AA 5 HOH C 1 601 34 HOH HOH . AA 5 HOH C 2 602 29 HOH HOH . AA 5 HOH C 3 603 2 HOH HOH . AA 5 HOH C 4 604 4 HOH HOH . AA 5 HOH C 5 605 10 HOH HOH . AA 5 HOH C 6 606 6 HOH HOH . BA 5 HOH D 1 601 21 HOH HOH . BA 5 HOH D 2 602 25 HOH HOH . BA 5 HOH D 3 603 30 HOH HOH . BA 5 HOH D 4 604 20 HOH HOH . BA 5 HOH D 5 605 18 HOH HOH . BA 5 HOH D 6 606 31 HOH HOH . BA 5 HOH D 7 607 16 HOH HOH . BA 5 HOH D 8 608 7 HOH HOH . BA 5 HOH D 9 609 36 HOH HOH . BA 5 HOH D 10 610 14 HOH HOH . BA 5 HOH D 11 611 8 HOH HOH . BA 5 HOH D 12 612 11 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 PB G4P . . . S 3 81.532 39.945 118.391 1 114.61 ? PB G4P 505 C 1 HETATM 2 O O1B G4P . . . S 3 80.064 39.728 118.103 1 105.32 ? O1B G4P 505 C 1 HETATM 3 O O2B G4P . . . S 3 81.674 40.911 119.554 1 88.89 ? O2B G4P 505 C 1 HETATM 4 O O3B G4P . . . S 3 82.193 40.529 117.156 1 115.33 ? O3B G4P 505 C 1 HETATM 5 O O3A G4P . . . S 3 82.23 38.498 118.802 1 68.39 ? O3A G4P 505 C 1 HETATM 6 P PA G4P . . . S 3 81.505 37.386 119.788 1 90.49 ? PA G4P 505 C 1 HETATM 7 O O1A G4P . . . S 3 80.032 37.23 119.497 1 102.29 ? O1A G4P 505 C 1 HETATM 8 O O2A G4P . . . S 3 81.686 37.735 121.246 1 67.63 ? O2A G4P 505 C 1 HETATM 9 O O5' G4P . . . S 3 82.301 35.968 119.483 1 102.46 ? O5' G4P 505 C 1 HETATM 10 C C5' G4P . . . S 3 83.641 36.195 119.141 1 79.87 ? C5' G4P 505 C 1 HETATM 11 C C4' G4P . . . S 3 84.321 34.917 119.498 1 88.81 ? C4' G4P 505 C 1 HETATM 12 O O4' G4P . . . S 3 84.081 34.079 118.557 1 83.77 ? O4' G4P 505 C 1 HETATM 13 C C3' G4P . . . S 3 85.947 35.159 119.735 1 83.96 ? C3' G4P 505 C 1 HETATM 14 O O3' G4P . . . S 3 86.162 34.489 121.081 1 109.17 ? O3' G4P 505 C 1 HETATM 15 C C2' G4P . . . S 3 86.473 34.564 118.785 1 93.53 ? C2' G4P 505 C 1 HETATM 16 O O2' G4P . . . S 3 87.926 34.231 118.885 1 128.11 ? O2' G4P 505 C 1 HETATM 17 C C1' G4P . . . S 3 85.389 33.359 118.531 1 82.69 ? C1' G4P 505 C 1 HETATM 18 N N9 G4P . . . S 3 85.574 32.393 117.627 1 89.84 ? N9 G4P 505 C 1 HETATM 19 C C8 G4P . . . S 3 85.759 33.036 116.47 1 92.07 ? C8 G4P 505 C 1 HETATM 20 N N7 G4P . . . S 3 85.929 32.025 115.542 1 84.18 ? N7 G4P 505 C 1 HETATM 21 C C5 G4P . . . S 3 85.773 30.837 116.179 1 83.55 ? C5 G4P 505 C 1 HETATM 22 C C6 G4P . . . S 3 85.799 29.334 115.816 1 74.74 ? C6 G4P 505 C 1 HETATM 23 O O6 G4P . . . S 3 86.002 28.988 114.693 1 85.38 ? O6 G4P 505 C 1 HETATM 24 N N1 G4P . . . S 3 85.579 28.289 116.8 1 82.62 ? N1 G4P 505 C 1 HETATM 25 C C2 G4P . . . S 3 85.326 28.642 118.174 1 87.76 ? C2 G4P 505 C 1 HETATM 26 N N2 G4P . . . S 3 85.091 27.713 119.258 1 82.67 ? N2 G4P 505 C 1 HETATM 27 N N3 G4P . . . S 3 85.304 30.059 118.506 1 85.76 ? N3 G4P 505 C 1 HETATM 28 C C4 G4P . . . S 3 85.534 31.11 117.48 1 83.68 ? C4 G4P 505 C 1 HETATM 29 P PC G4P . . . S 3 87.558 33.666 121.598 1 91.98 ? PC G4P 505 C 1 HETATM 30 O O1C G4P . . . S 3 88.67 34.689 121.629 1 95.71 ? O1C G4P 505 C 1 HETATM 31 O O2C G4P . . . S 3 87.407 33.08 122.979 1 94.85 ? O2C G4P 505 C 1 HETATM 32 O O3C G4P . . . S 3 87.925 32.433 120.535 1 115.42 ? O3C G4P 505 C 1 HETATM 33 P PD G4P . . . S 3 89.478 32.004 120.073 1 185.7 ? PD G4P 505 C 1 HETATM 34 O O1D G4P . . . S 3 89.434 31.258 118.75 1 143.3 ? O1D G4P 505 C 1 HETATM 35 O O2D G4P . . . S 3 90.097 31.135 121.146 1 196.12 ? O2D G4P 505 C 1 HETATM 36 O O3D G4P . . . S 3 90.311 33.258 119.893 1 187.9 ? O3D G4P 505 C 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #