data_7O9F # _model_server_result.job_id o4MWmbnmUlc7oYyTNz2oUQ _model_server_result.datetime_utc '2025-03-04 20:37:30' _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 7o9f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 7O9F # _exptl.entry_id 7O9F _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 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 7O9F _cell.length_a 163.28 _cell.length_b 163.28 _cell.length_c 93.47 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7O9F _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,J 1 1 B,F,G,K 2 1 C,H,I 3 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 ? 2 D N N ? 2 F N N ? 2 H 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 123 A THR 115 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc2 D O3B G4P . A G4P 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? metalc ? metalc3 E MG MG . A MG 402 1_555 J O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc4 E MG MG . A MG 402 1_555 J O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc5 E MG MG . A MG 402 1_555 J O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc6 E MG MG . A MG 402 1_555 J O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc7 B OG1 THR 123 B THR 115 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc8 F O2B G4P . B G4P 401 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc9 G MG MG . B MG 402 1_555 K O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc10 G MG MG . B MG 402 1_555 K O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc11 G MG MG . B MG 402 1_555 K O HOH . B HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc12 C OG1 THR 123 C THR 115 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc13 H O1B G4P . C G4P 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? # _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 7O9F _atom_sites.fract_transf_matrix[1][1] 0.006124 _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] 0.006124 _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] 0.010699 _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 D 2 G4P A 1 401 301 G4P G4P . E 3 MG A 1 402 1 MG MG . F 2 G4P B 1 401 302 G4P G4P . G 3 MG B 1 402 2 MG MG . H 2 G4P C 1 401 303 G4P G4P . I 3 MG C 1 402 3 MG MG . J 4 HOH A 1 501 13 HOH HOH . J 4 HOH A 2 502 6 HOH HOH . J 4 HOH A 3 503 1 HOH HOH . J 4 HOH A 4 504 8 HOH HOH . J 4 HOH A 5 505 4 HOH HOH . J 4 HOH A 6 506 15 HOH HOH . J 4 HOH A 7 507 12 HOH HOH . J 4 HOH A 8 508 10 HOH HOH . J 4 HOH A 9 509 11 HOH HOH . J 4 HOH A 10 510 9 HOH HOH . K 4 HOH B 1 501 5 HOH HOH . K 4 HOH B 2 502 2 HOH HOH . K 4 HOH B 3 503 14 HOH HOH . K 4 HOH B 4 504 16 HOH HOH . K 4 HOH B 5 505 3 HOH HOH . K 4 HOH B 6 506 7 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 . . . F 2 -17.395 49.149 12.858 1 67.64 ? PB G4P 401 B 1 HETATM 2 O O1B G4P . . . F 2 -16.647 50.298 13.488 1 75.19 ? O1B G4P 401 B 1 HETATM 3 O O2B G4P . . . F 2 -18.812 49.569 12.551 1 67.7 ? O2B G4P 401 B 1 HETATM 4 O O3B G4P . . . F 2 -17.404 47.97 13.804 1 76.85 ? O3B G4P 401 B 1 HETATM 5 O O3A G4P . . . F 2 -16.629 48.704 11.476 1 71.13 ? O3A G4P 401 B 1 HETATM 6 P PA G4P . . . F 2 -16.754 49.464 10.024 1 87.94 ? PA G4P 401 B 1 HETATM 7 O O1A G4P . . . F 2 -18.031 49.059 9.329 1 66.67 ? O1A G4P 401 B 1 HETATM 8 O O2A G4P . . . F 2 -16.727 50.959 10.225 1 70.69 ? O2A G4P 401 B 1 HETATM 9 O O5' G4P . . . F 2 -15.46 49.005 9.121 1 73.45 ? O5' G4P 401 B 1 HETATM 10 C C5' G4P . . . F 2 -14.185 49.064 9.695 1 57.77 ? C5' G4P 401 B 1 HETATM 11 C C4' G4P . . . F 2 -13.128 48.905 8.571 1 54.84 ? C4' G4P 401 B 1 HETATM 12 O O4' G4P . . . F 2 -12.953 47.635 8.313 1 65.86 ? O4' G4P 401 B 1 HETATM 13 C C3' G4P . . . F 2 -13.67 49.553 7.278 1 61.11 ? C3' G4P 401 B 1 HETATM 14 O O3' G4P . . . F 2 -12.734 50.262 6.592 1 75.43 ? O3' G4P 401 B 1 HETATM 15 C C2' G4P . . . F 2 -14.108 48.368 6.399 1 69.07 ? C2' G4P 401 B 1 HETATM 16 O O2' G4P . . . F 2 -13.877 48.715 4.965 1 69.54 ? O2' G4P 401 B 1 HETATM 17 C C1' G4P . . . F 2 -13.329 47.385 6.759 1 61.16 ? C1' G4P 401 B 1 HETATM 18 N N9 G4P . . . F 2 -14.002 46.118 6.634 1 58.74 ? N9 G4P 401 B 1 HETATM 19 C C8 G4P . . . F 2 -15.148 45.638 7.155 1 74.09 ? C8 G4P 401 B 1 HETATM 20 N N7 G4P . . . F 2 -15.309 44.373 6.718 1 57.6 ? N7 G4P 401 B 1 HETATM 21 C C5 G4P . . . F 2 -14.276 44.071 5.938 1 66.41 ? C5 G4P 401 B 1 HETATM 22 C C6 G4P . . . F 2 -13.906 42.798 5.166 1 68.96 ? C6 G4P 401 B 1 HETATM 23 O O6 G4P . . . F 2 -14.614 41.848 5.203 1 59.77 ? O6 G4P 401 B 1 HETATM 24 N N1 G4P . . . F 2 -12.705 42.758 4.392 1 64.03 ? N1 G4P 401 B 1 HETATM 25 C C2 G4P . . . F 2 -11.849 43.914 4.342 1 45.38 ? C2 G4P 401 B 1 HETATM 26 N N2 G4P . . . F 2 -10.63 43.877 3.557 1 73.45 ? N2 G4P 401 B 1 HETATM 27 N N3 G4P . . . F 2 -12.205 45.122 5.082 1 65.2 ? N3 G4P 401 B 1 HETATM 28 C C4 G4P . . . F 2 -13.459 45.162 5.888 1 63.35 ? C4 G4P 401 B 1 HETATM 29 P PC G4P . . . F 2 -11.587 51.199 7.321 1 59.25 ? PC G4P 401 B 1 HETATM 30 O O1C G4P . . . F 2 -12.139 51.941 8.515 1 63.73 ? O1C G4P 401 B 1 HETATM 31 O O2C G4P . . . F 2 -11.082 52.204 6.316 1 66.51 ? O2C G4P 401 B 1 HETATM 32 O O3C G4P . . . F 2 -10.333 50.238 7.785 1 90.97 ? O3C G4P 401 B 1 HETATM 33 P PD G4P . . . F 2 -8.9 50.824 8.342 1 100.5 ? PD G4P 401 B 1 HETATM 34 O O1D G4P . . . F 2 -7.886 49.708 8.386 1 101.01 ? O1D G4P 401 B 1 HETATM 35 O O2D G4P . . . F 2 -8.408 51.911 7.418 1 89.4 ? O2D G4P 401 B 1 HETATM 36 O O3D G4P . . . F 2 -9.101 51.391 9.727 1 98.87 ? O3D G4P 401 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 36 #