data_7O9G # _model_server_result.job_id bG78nst8UtxzsybUU0qrkw _model_server_result.datetime_utc '2025-03-04 21:00:38' _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 7o9g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7O9G # _exptl.entry_id 7O9G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 603.16 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5',3'-TETRAPHOSPHATE" _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 96.27 _cell.angle_gamma 90 _cell.entry_id 7O9G _cell.length_a 48.63 _cell.length_b 38.2 _cell.length_c 78.44 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7O9G _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 metalc ? metalc1 A OG1 THR 115 A THR 114 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc2 B O2B G4P . A G4P 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? # _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 70 n n PB O2B G4P sing 71 n n PB O3B G4P sing 72 n n PB O3A G4P sing 73 n n O2B HOB2 G4P sing 74 n n O3B HOB3 G4P sing 75 n n O3A PA G4P sing 76 n n PA O1A G4P doub 77 n n PA O2A G4P sing 78 n n PA O5' G4P sing 79 n n O2A HOA2 G4P sing 80 n n O5' C5' G4P sing 81 n n C5' C4' G4P sing 82 n n C5' H5' G4P sing 83 n n C5' "H5''" G4P sing 84 n n C4' O4' G4P sing 85 n n C4' C3' G4P sing 86 n n C4' H4' G4P sing 87 n n O4' C1' G4P sing 88 n n C3' O3' G4P sing 89 n n C3' C2' G4P sing 90 n n C3' H3' G4P sing 91 n n O3' PC G4P sing 92 n n C2' O2' G4P sing 93 n n C2' C1' G4P sing 94 n n C2' H2' G4P sing 95 n n O2' HO2' G4P sing 96 n n C1' N9 G4P sing 97 n n C1' H1' G4P sing 98 n n N9 C8 G4P sing 99 n y N9 C4 G4P sing 100 n y C8 N7 G4P doub 101 n y C8 H8 G4P sing 102 n n N7 C5 G4P sing 103 n y C5 C6 G4P sing 104 n n C5 C4 G4P doub 105 n y C6 O6 G4P doub 106 n n C6 N1 G4P sing 107 n n N1 C2 G4P sing 108 n n N1 HN1 G4P sing 109 n n C2 N2 G4P sing 110 n n C2 N3 G4P doub 111 n n N2 HN21 G4P sing 112 n n N2 HN22 G4P sing 113 n n N3 C4 G4P sing 114 n n PC O1C G4P doub 115 n n PC O2C G4P sing 116 n n PC O3C G4P sing 117 n n O2C H2C G4P sing 118 n n O3C PD G4P sing 119 n n PD O1D G4P doub 120 n n PD O2D G4P sing 121 n n PD O3D G4P sing 122 n n O2D H2D G4P sing 123 n n O3D H3D G4P sing 124 n n # _atom_sites.entry_id 7O9G _atom_sites.fract_transf_matrix[1][1] 0.020563 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00226 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026178 _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] 0.012825 _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 B 2 G4P A 1 401 301 G4P G4P . C 3 MG A 1 402 1 MG MG . D 4 HOH A 1 501 7 HOH HOH . D 4 HOH A 2 502 1 HOH HOH . D 4 HOH A 3 503 9 HOH HOH . D 4 HOH A 4 504 6 HOH HOH . D 4 HOH A 5 505 4 HOH HOH . D 4 HOH A 6 506 2 HOH HOH . D 4 HOH A 7 507 3 HOH HOH . D 4 HOH A 8 508 8 HOH HOH . D 4 HOH A 9 509 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 PB G4P . . . B 2 -10.032 -12.449 20.119 1 49.79 ? PB G4P 401 A 1 HETATM 2 O O1B G4P . . . B 2 -10.14 -13.91 20.417 1 54.79 ? O1B G4P 401 A 1 HETATM 3 O O2B G4P . . . B 2 -11.104 -11.897 19.252 1 52.28 ? O2B G4P 401 A 1 HETATM 4 O O3B G4P . . . B 2 -8.66 -12.007 19.721 1 49.34 ? O3B G4P 401 A 1 HETATM 5 O O3A G4P . . . B 2 -10.312 -11.738 21.521 1 49.18 ? O3A G4P 401 A 1 HETATM 6 P PA G4P . . . B 2 -11.772 -11.489 22.126 1 45.39 ? PA G4P 401 A 1 HETATM 7 O O1A G4P . . . B 2 -12.44 -10.377 21.386 1 45.2 ? O1A G4P 401 A 1 HETATM 8 O O2A G4P . . . B 2 -12.469 -12.799 22.316 1 54.31 ? O2A G4P 401 A 1 HETATM 9 O O5' G4P . . . B 2 -11.413 -10.905 23.562 1 53.55 ? O5' G4P 401 A 1 HETATM 10 C C5' G4P . . . B 2 -10.678 -11.693 24.486 1 53.61 ? C5' G4P 401 A 1 HETATM 11 C C4' G4P . . . B 2 -10.661 -11.003 25.833 1 54.29 ? C4' G4P 401 A 1 HETATM 12 O O4' G4P . . . B 2 -10.022 -9.748 25.727 1 53.31 ? O4' G4P 401 A 1 HETATM 13 C C3' G4P . . . B 2 -12.042 -10.72 26.382 1 59.81 ? C3' G4P 401 A 1 HETATM 14 O O3' G4P . . . B 2 -12.077 -11.263 27.683 1 63.4 ? O3' G4P 401 A 1 HETATM 15 C C2' G4P . . . B 2 -12.168 -9.22 26.442 1 54.23 ? C2' G4P 401 A 1 HETATM 16 O O2' G4P . . . B 2 -12.954 -8.799 27.555 1 62.15 ? O2' G4P 401 A 1 HETATM 17 C C1' G4P . . . B 2 -10.716 -8.817 26.544 1 53.82 ? C1' G4P 401 A 1 HETATM 18 N N9 G4P . . . B 2 -10.378 -7.467 26.061 1 52.2 ? N9 G4P 401 A 1 HETATM 19 C C8 G4P . . . B 2 -10.371 -7.041 24.791 1 51.25 ? C8 G4P 401 A 1 HETATM 20 N N7 G4P . . . B 2 -9.973 -5.752 24.731 1 46.64 ? N7 G4P 401 A 1 HETATM 21 C C5 G4P . . . B 2 -9.709 -5.355 25.982 1 47.55 ? C5 G4P 401 A 1 HETATM 22 C C6 G4P . . . B 2 -9.242 -4.125 26.636 1 48.91 ? C6 G4P 401 A 1 HETATM 23 O O6 G4P . . . B 2 -9.004 -3.118 25.963 1 48.07 ? O6 G4P 401 A 1 HETATM 24 N N1 G4P . . . B 2 -9.093 -4.113 27.956 1 49.36 ? N1 G4P 401 A 1 HETATM 25 C C2 G4P . . . B 2 -9.352 -5.196 28.703 1 49.52 ? C2 G4P 401 A 1 HETATM 26 N N2 G4P . . . B 2 -9.187 -5.152 30.041 1 53.91 ? N2 G4P 401 A 1 HETATM 27 N N3 G4P . . . B 2 -9.78 -6.359 28.174 1 51.17 ? N3 G4P 401 A 1 HETATM 28 C C4 G4P . . . B 2 -9.97 -6.491 26.85 1 48.54 ? C4 G4P 401 A 1 HETATM 29 P PC G4P . . . B 2 -13.244 -12.195 28.238 1 79.81 ? PC G4P 401 A 1 HETATM 30 O O1C G4P . . . B 2 -13.794 -13.081 27.154 1 80.49 ? O1C G4P 401 A 1 HETATM 31 O O2C G4P . . . B 2 -14.16 -11.302 29.03 1 79.35 ? O2C G4P 401 A 1 HETATM 32 O O3C G4P . . . B 2 -12.441 -13.111 29.271 1 92.26 ? O3C G4P 401 A 1 HETATM 33 P PD G4P . . . B 2 -11.014 -13.739 28.889 1 114.96 ? PD G4P 401 A 1 HETATM 34 O O1D G4P . . . B 2 -10.026 -12.631 29.155 1 95.71 ? O1D G4P 401 A 1 HETATM 35 O O2D G4P . . . B 2 -10.879 -14.897 29.845 1 109.86 ? O2D G4P 401 A 1 HETATM 36 O O3D G4P . . . B 2 -11.149 -14.155 27.448 1 86.23 ? O3D G4P 401 A 1 HETATM 37 H H5' G4P . . . B 2 -11.123 -12.683 24.592 1 64.08 ? H5' G4P 401 A 1 HETATM 38 H "H5''" G4P . . . B 2 -9.652 -11.816 24.135 1 64.08 ? "H5''" G4P 401 A 1 HETATM 39 H H4' G4P . . . B 2 -10.115 -11.634 26.546 1 64.9 ? H4' G4P 401 A 1 HETATM 40 H H3' G4P . . . B 2 -12.824 -11.139 25.736 1 71.53 ? H3' G4P 401 A 1 HETATM 41 H H2' G4P . . . B 2 -12.592 -8.85 25.5 1 64.83 ? H2' G4P 401 A 1 HETATM 42 H HO2' G4P . . . B 2 -12.577 -9.135 28.38 1 74.33 ? HO2' G4P 401 A 1 HETATM 43 H H1' G4P . . . B 2 -10.378 -8.938 27.582 1 64.33 ? H1' G4P 401 A 1 HETATM 44 H H8 G4P . . . B 2 -10.657 -7.639 23.936 1 61.25 ? H8 G4P 401 A 1 HETATM 45 H HN1 G4P . . . B 2 -8.767 -3.239 28.41 1 58.98 ? HN1 G4P 401 A 1 HETATM 46 H HN21 G4P . . . B 2 -9.383 -5.974 30.594 1 64.45 ? HN21 G4P 401 A 1 HETATM 47 H HN22 G4P . . . B 2 -8.87 -4.309 30.495 1 64.45 ? HN22 G4P 401 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 575 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 47 #