data_2QAG # _model_server_result.job_id d9BdrcdAVfbGYXLcLtf9IQ _model_server_result.datetime_utc '2024-11-19 01:26:19' _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 2qag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":419}' # _entry.id 2QAG # _exptl.entry_id 2QAG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 2QAG _cell.length_a 252.515 _cell.length_b 252.515 _cell.length_c 156.485 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QAG _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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' 5_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 252.515 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 F N 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 2QAG _atom_sites.fract_transf_matrix[1][1] 0.00396 _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] 0.00396 _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] 0.00639 _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 4 GDP A 1 362 362 GDP GDP . E 5 GTP B 1 428 428 GTP GTP . F 4 GDP C 1 419 419 GDP GDP . # 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 . . . F 4 7.996 75.045 9.045 1 98.83 ? PB GDP 419 C 1 HETATM 2 O O1B GDP . . . F 4 8.48 74.843 10.461 1 95.89 ? O1B GDP 419 C 1 HETATM 3 O O2B GDP . . . F 4 6.601 75.623 9.067 1 100.69 ? O2B GDP 419 C 1 HETATM 4 O O3B GDP . . . F 4 8.924 75.996 8.327 1 97.82 ? O3B GDP 419 C 1 HETATM 5 O O3A GDP . . . F 4 7.979 73.63 8.277 1 96.34 ? O3A GDP 419 C 1 HETATM 6 P PA GDP . . . F 4 7.536 72.288 9.047 1 96.32 ? PA GDP 419 C 1 HETATM 7 O O1A GDP . . . F 4 8.29 71.094 8.511 1 96.67 ? O1A GDP 419 C 1 HETATM 8 O O2A GDP . . . F 4 7.754 72.432 10.534 1 95.92 ? O2A GDP 419 C 1 HETATM 9 O O5' GDP . . . F 4 5.965 72.161 8.715 1 93.92 ? O5' GDP 419 C 1 HETATM 10 C C5' GDP . . . F 4 5.491 71.144 7.834 1 91.2 ? C5' GDP 419 C 1 HETATM 11 C C4' GDP . . . F 4 4.7 70.112 8.628 1 89.68 ? C4' GDP 419 C 1 HETATM 12 O O4' GDP . . . F 4 4.106 69.171 7.729 1 87.98 ? O4' GDP 419 C 1 HETATM 13 C C3' GDP . . . F 4 5.607 69.341 9.577 1 90.22 ? C3' GDP 419 C 1 HETATM 14 O O3' GDP . . . F 4 5.136 69.497 10.92 1 91.13 ? O3' GDP 419 C 1 HETATM 15 C C2' GDP . . . F 4 5.505 67.882 9.17 1 90.74 ? C2' GDP 419 C 1 HETATM 16 O O2' GDP . . . F 4 4.968 67.119 10.258 1 93.13 ? O2' GDP 419 C 1 HETATM 17 C C1' GDP . . . F 4 4.54 67.834 7.993 1 87.83 ? C1' GDP 419 C 1 HETATM 18 N N9 GDP . . . F 4 5.242 67.296 6.8 1 87.3 ? N9 GDP 419 C 1 HETATM 19 C C8 GDP . . . F 4 6.471 67.653 6.382 1 85.55 ? C8 GDP 419 C 1 HETATM 20 N N7 GDP . . . F 4 6.822 66.976 5.259 1 83.8 ? N7 GDP 419 C 1 HETATM 21 C C5 GDP . . . F 4 5.799 66.162 4.941 1 84.91 ? C5 GDP 419 C 1 HETATM 22 C C6 GDP . . . F 4 5.51 65.175 3.875 1 85.74 ? C6 GDP 419 C 1 HETATM 23 O O6 GDP . . . F 4 6.344 64.937 2.974 1 87.5 ? O6 GDP 419 C 1 HETATM 24 N N1 GDP . . . F 4 4.329 64.544 3.905 1 85.1 ? N1 GDP 419 C 1 HETATM 25 C C2 GDP . . . F 4 3.412 64.78 4.862 1 84.51 ? C2 GDP 419 C 1 HETATM 26 N N2 GDP . . . F 4 2.241 64.099 4.82 1 85.63 ? N2 GDP 419 C 1 HETATM 27 N N3 GDP . . . F 4 3.609 65.67 5.869 1 84.84 ? N3 GDP 419 C 1 HETATM 28 C C4 GDP . . . F 4 4.76 66.377 5.959 1 85.8 ? C4 GDP 419 C 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #