data_5A9X # _model_server_result.job_id LX_j9L76X0chsKMHieZVeg _model_server_result.datetime_utc '2025-07-12 06:06:54' _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 5a9x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1603}' # _entry.id 5A9X # _exptl.entry_id 5A9X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 5A9X _cell.length_a 241.946 _cell.length_b 241.946 _cell.length_c 241.946 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A9X _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 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 _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 # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 5A9X _atom_sites.fract_transf_matrix[1][1] 0.004133 _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] 0.004133 _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] 0.004133 _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 GDP A 1 1603 1603 GDP GDP . C 3 HOH A 1 2001 2001 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 GDP . . . B 2 -5.613 -21.069 32.142 1 262.8 ? PB GDP 1603 A 1 HETATM 2 O O1B GDP . . . B 2 -6.421 -19.945 32.746 1 250.51 ? O1B GDP 1603 A 1 HETATM 3 O O2B GDP . . . B 2 -5.246 -22.165 33.114 1 253.61 ? O2B GDP 1603 A 1 HETATM 4 O O3B GDP . . . B 2 -6.129 -21.562 30.811 1 249.61 ? O3B GDP 1603 A 1 HETATM 5 O O3A GDP . . . B 2 -4.203 -20.382 31.781 1 261.76 ? O3A GDP 1603 A 1 HETATM 6 P PA GDP . . . B 2 -3.746 -19.022 32.511 1 250.73 ? PA GDP 1603 A 1 HETATM 7 O O1A GDP . . . B 2 -4.294 -19.034 33.918 1 232.25 ? O1A GDP 1603 A 1 HETATM 8 O O2A GDP . . . B 2 -4.057 -17.865 31.592 1 242.92 ? O2A GDP 1603 A 1 HETATM 9 O O5' GDP . . . B 2 -2.146 -19.185 32.592 1 250.2 ? O5' GDP 1603 A 1 HETATM 10 C C5' GDP . . . B 2 -1.542 -19.859 33.694 1 236.69 ? C5' GDP 1603 A 1 HETATM 11 C C4' GDP . . . B 2 -0.937 -18.834 34.645 1 236.54 ? C4' GDP 1603 A 1 HETATM 12 O O4' GDP . . . B 2 0.333 -18.406 34.147 1 236.72 ? O4' GDP 1603 A 1 HETATM 13 C C3' GDP . . . B 2 -1.825 -17.607 34.771 1 231.77 ? C3' GDP 1603 A 1 HETATM 14 O O3' GDP . . . B 2 -2.22 -17.426 36.134 1 252.48 ? O3' GDP 1603 A 1 HETATM 15 C C2' GDP . . . B 2 -0.991 -16.429 34.311 1 230.26 ? C2' GDP 1603 A 1 HETATM 16 O O2' GDP . . . B 2 -0.844 -15.486 35.377 1 245.99 ? O2' GDP 1603 A 1 HETATM 17 C C1' GDP . . . B 2 0.367 -16.993 33.924 1 227.63 ? C1' GDP 1603 A 1 HETATM 18 N N9 GDP . . . B 2 0.631 -16.72 32.489 1 215.02 ? N9 GDP 1603 A 1 HETATM 19 C C8 GDP . . . B 2 0.004 -17.299 31.449 1 209.11 ? C8 GDP 1603 A 1 HETATM 20 N N7 GDP . . . B 2 0.479 -16.83 30.266 1 197.03 ? N7 GDP 1603 A 1 HETATM 21 C C5 GDP . . . B 2 1.436 -15.927 30.546 1 197.23 ? C5 GDP 1603 A 1 HETATM 22 C C6 GDP . . . B 2 2.343 -15.054 29.764 1 206.59 ? C6 GDP 1603 A 1 HETATM 23 O O6 GDP . . . B 2 2.32 -15.057 28.514 1 200.45 ? O6 GDP 1603 A 1 HETATM 24 N N1 GDP . . . B 2 3.188 -14.263 30.437 1 224.58 ? N1 GDP 1603 A 1 HETATM 25 C C2 GDP . . . B 2 3.236 -14.239 31.783 1 226.73 ? C2 GDP 1603 A 1 HETATM 26 N N2 GDP . . . B 2 4.121 -13.409 32.385 1 231.77 ? N2 GDP 1603 A 1 HETATM 27 N N3 GDP . . . B 2 2.435 -15.011 32.562 1 218.51 ? N3 GDP 1603 A 1 HETATM 28 C C4 GDP . . . B 2 1.533 -15.858 32.012 1 208.17 ? C4 GDP 1603 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #