data_5A9Y # _model_server_result.job_id w2I4sTcxBvFUNZEWVV70HA _model_server_result.datetime_utc '2025-07-15 14:42:22' _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 5a9y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1603}' # _entry.id 5A9Y # _exptl.entry_id 5A9Y _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 90 _cell.angle_gamma 90 _cell.entry_id 5A9Y _cell.length_a 244.31 _cell.length_b 244.31 _cell.length_c 244.31 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A9Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 214 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 3 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 28_554 x,-y,-z-1/2 1 0 0 0 -1 0 0 0 -1 0 0 -122.155 # _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 # _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 83 n n PB O2B G4P sing 84 n n PB O3B G4P sing 85 n n PB O3A G4P sing 86 n n O2B HOB2 G4P sing 87 n n O3B HOB3 G4P sing 88 n n O3A PA G4P sing 89 n n PA O1A G4P doub 90 n n PA O2A G4P sing 91 n n PA O5' G4P sing 92 n n O2A HOA2 G4P sing 93 n n O5' C5' G4P sing 94 n n C5' C4' G4P sing 95 n n C5' H5' G4P sing 96 n n C5' "H5''" G4P sing 97 n n C4' O4' G4P sing 98 n n C4' C3' G4P sing 99 n n C4' H4' G4P sing 100 n n O4' C1' G4P sing 101 n n C3' O3' G4P sing 102 n n C3' C2' G4P sing 103 n n C3' H3' G4P sing 104 n n O3' PC G4P sing 105 n n C2' O2' G4P sing 106 n n C2' C1' G4P sing 107 n n C2' H2' G4P sing 108 n n O2' HO2' G4P sing 109 n n C1' N9 G4P sing 110 n n C1' H1' G4P sing 111 n n N9 C8 G4P sing 112 n y N9 C4 G4P sing 113 n y C8 N7 G4P doub 114 n y C8 H8 G4P sing 115 n n N7 C5 G4P sing 116 n y C5 C6 G4P sing 117 n n C5 C4 G4P doub 118 n y C6 O6 G4P doub 119 n n C6 N1 G4P sing 120 n n N1 C2 G4P sing 121 n n N1 HN1 G4P sing 122 n n C2 N2 G4P sing 123 n n C2 N3 G4P doub 124 n n N2 HN21 G4P sing 125 n n N2 HN22 G4P sing 126 n n N3 C4 G4P sing 127 n n PC O1C G4P doub 128 n n PC O2C G4P sing 129 n n PC O3C G4P sing 130 n n O2C H2C G4P sing 131 n n O3C PD G4P sing 132 n n PD O1D G4P doub 133 n n PD O2D G4P sing 134 n n PD O3D G4P sing 135 n n O2D H2D G4P sing 136 n n O3D H3D G4P sing 137 n n # _atom_sites.entry_id 5A9Y _atom_sites.fract_transf_matrix[1][1] 0.004093 _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] 0.004093 _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] 0.004093 _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 1603 1603 G4P G4P . C 3 HOH A 1 2001 2001 HOH HOH . C 3 HOH A 2 2002 2002 HOH HOH . C 3 HOH A 3 2003 2003 HOH HOH . C 3 HOH A 4 2004 2004 HOH HOH . C 3 HOH A 5 2005 2005 HOH HOH . C 3 HOH A 6 2006 2006 HOH HOH . C 3 HOH A 7 2007 2007 HOH HOH . C 3 HOH A 8 2008 2008 HOH HOH . C 3 HOH A 9 2009 2009 HOH HOH . C 3 HOH A 10 2010 2010 HOH HOH . C 3 HOH A 11 2011 2011 HOH HOH . C 3 HOH A 12 2012 2012 HOH HOH . C 3 HOH A 13 2013 2013 HOH HOH . C 3 HOH A 14 2014 2014 HOH HOH . C 3 HOH A 15 2015 2015 HOH HOH . C 3 HOH A 16 2016 2016 HOH HOH . C 3 HOH A 17 2017 2017 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 31.362 -6.595 -21.713 1 475.82 ? PB G4P 1603 A 1 HETATM 2 O O1B G4P . . . B 2 31.316 -6.619 -23.222 1 459.31 ? O1B G4P 1603 A 1 HETATM 3 O O2B G4P . . . B 2 31.573 -7.941 -21.06 1 500 ? O2B G4P 1603 A 1 HETATM 4 O O3B G4P . . . B 2 30.237 -5.776 -21.136 1 468.97 ? O3B G4P 1603 A 1 HETATM 5 O O3A G4P . . . B 2 32.683 -5.766 -21.309 1 433.01 ? O3A G4P 1603 A 1 HETATM 6 P PA G4P . . . B 2 32.582 -4.168 -21.25 1 340.19 ? PA G4P 1603 A 1 HETATM 7 O O1A G4P . . . B 2 31.831 -3.821 -22.509 1 298.3 ? O1A G4P 1603 A 1 HETATM 8 O O2A G4P . . . B 2 32.035 -3.769 -19.907 1 328.23 ? O2A G4P 1603 A 1 HETATM 9 O O5' G4P . . . B 2 34.118 -3.677 -21.319 1 351.74 ? O5' G4P 1603 A 1 HETATM 10 C C5' G4P . . . B 2 35.011 -3.806 -20.203 1 357.42 ? C5' G4P 1603 A 1 HETATM 11 C C4' G4P . . . B 2 35.521 -2.437 -19.747 1 347.73 ? C4' G4P 1603 A 1 HETATM 12 O O4' G4P . . . B 2 34.477 -1.457 -19.772 1 337.54 ? O4' G4P 1603 A 1 HETATM 13 C C3' G4P . . . B 2 36.075 -2.449 -18.325 1 343.76 ? C3' G4P 1603 A 1 HETATM 14 O O3' G4P . . . B 2 37.467 -2.128 -18.374 1 337.89 ? O3' G4P 1603 A 1 HETATM 15 C C2' G4P . . . B 2 35.257 -1.423 -17.551 1 341.06 ? C2' G4P 1603 A 1 HETATM 16 O O2' G4P . . . B 2 36.093 -0.603 -16.728 1 344.63 ? O2' G4P 1603 A 1 HETATM 17 C C1' G4P . . . B 2 34.525 -0.61 -18.616 1 336.11 ? C1' G4P 1603 A 1 HETATM 18 N N9 G4P . . . B 2 33.149 -0.166 -18.21 1 317.48 ? N9 G4P 1603 A 1 HETATM 19 C C8 G4P . . . B 2 31.987 -0.683 -18.661 1 327.15 ? C8 G4P 1603 A 1 HETATM 20 N N7 G4P . . . B 2 30.913 -0.054 -18.117 1 333.36 ? N7 G4P 1603 A 1 HETATM 21 C C5 G4P . . . B 2 31.366 0.903 -17.293 1 303.02 ? C5 G4P 1603 A 1 HETATM 22 C C6 G4P . . . B 2 30.759 1.931 -16.4 1 286.95 ? C6 G4P 1603 A 1 HETATM 23 O O6 G4P . . . B 2 29.519 2.066 -16.276 1 260.07 ? O6 G4P 1603 A 1 HETATM 24 N N1 G4P . . . B 2 31.592 2.727 -15.716 1 291.86 ? N1 G4P 1603 A 1 HETATM 25 C C2 G4P . . . B 2 32.937 2.627 -15.81 1 283.55 ? C2 G4P 1603 A 1 HETATM 26 N N2 G4P . . . B 2 33.71 3.475 -15.084 1 288.67 ? N2 G4P 1603 A 1 HETATM 27 N N3 G4P . . . B 2 33.553 1.706 -16.608 1 288.16 ? N3 G4P 1603 A 1 HETATM 28 C C4 G4P . . . B 2 32.841 0.829 -17.361 1 297.56 ? C4 G4P 1603 A 1 HETATM 29 P PC G4P . . . B 2 38.542 -2.942 -17.499 1 355.04 ? PC G4P 1603 A 1 HETATM 30 O O1C G4P . . . B 2 38.128 -2.795 -16.05 1 357.31 ? O1C G4P 1603 A 1 HETATM 31 O O2C G4P . . . B 2 39.915 -2.501 -17.963 1 348.05 ? O2C G4P 1603 A 1 HETATM 32 O O3C G4P . . . B 2 38.317 -4.48 -17.957 1 427.49 ? O3C G4P 1603 A 1 HETATM 33 P PD G4P . . . B 2 38.129 -5.715 -16.922 1 498.61 ? PD G4P 1603 A 1 HETATM 34 O O1D G4P . . . B 2 39.299 -5.601 -15.97 1 500 ? O1D G4P 1603 A 1 HETATM 35 O O2D G4P . . . B 2 38.169 -6.942 -17.806 1 500 ? O2D G4P 1603 A 1 HETATM 36 O O3D G4P . . . B 2 36.785 -5.486 -16.265 1 478.09 ? O3D G4P 1603 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #