data_8U7L # _model_server_result.job_id xfcXLwcYR3VzDmVyELgtTQ _model_server_result.datetime_utc '2024-11-28 14:33:01' _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 8u7l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2601}' # _entry.id 8U7L # _exptl.entry_id 8U7L _exptl.method 'ELECTRON MICROSCOPY' # _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 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 8U7L _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8U7L _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _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 ? _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 C N N ? 2 E 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 8U7L _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 C 2 GDP B 1 2601 2601 GDP GDP . D 3 T3X B 1 2602 2602 T3X LIG . E 2 GDP A 1 2601 2601 GDP GDP . F 3 T3X A 1 2602 2602 T3X LIG . # 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 . . . E 2 274.742 250.021 324.829 1 77.12 ? PB GDP 2601 A 1 HETATM 2 O O1B GDP . . . E 2 273.555 250.224 323.923 1 77.12 ? O1B GDP 2601 A 1 HETATM 3 O O2B GDP . . . E 2 275.52 248.805 324.408 1 77.12 ? O2B GDP 2601 A 1 HETATM 4 O O3B GDP . . . E 2 275.637 251.23 324.749 1 77.12 ? O3B GDP 2601 A 1 HETATM 5 O O3A GDP . . . E 2 274.254 249.811 326.343 1 77.12 ? O3A GDP 2601 A 1 HETATM 6 P PA GDP . . . E 2 275.363 249.701 327.5 1 77.12 ? PA GDP 2601 A 1 HETATM 7 O O1A GDP . . . E 2 276.175 248.444 327.318 1 77.12 ? O1A GDP 2601 A 1 HETATM 8 O O2A GDP . . . E 2 276.259 250.913 327.504 1 77.12 ? O2A GDP 2601 A 1 HETATM 9 O O5' GDP . . . E 2 274.517 249.634 328.864 1 77.12 ? O5' GDP 2601 A 1 HETATM 10 C C5' GDP . . . E 2 275.208 249.791 330.098 1 77.12 ? C5' GDP 2601 A 1 HETATM 11 C C4' GDP . . . E 2 274.236 249.816 331.268 1 77.12 ? C4' GDP 2601 A 1 HETATM 12 O O4' GDP . . . E 2 273.778 248.491 331.542 1 77.12 ? O4' GDP 2601 A 1 HETATM 13 C C3' GDP . . . E 2 274.923 250.334 332.519 1 77.12 ? C3' GDP 2601 A 1 HETATM 14 O O3' GDP . . . E 2 274.279 251.531 332.961 1 77.12 ? O3' GDP 2601 A 1 HETATM 15 C C2' GDP . . . E 2 274.762 249.254 333.566 1 77.12 ? C2' GDP 2601 A 1 HETATM 16 O O2' GDP . . . E 2 274.146 249.805 334.732 1 77.12 ? O2' GDP 2601 A 1 HETATM 17 C C1' GDP . . . E 2 273.854 248.21 332.941 1 77.12 ? C1' GDP 2601 A 1 HETATM 18 N N9 GDP . . . E 2 274.41 246.85 333.138 1 77.12 ? N9 GDP 2601 A 1 HETATM 19 C C8 GDP . . . E 2 275.129 246.17 332.23 1 77.12 ? C8 GDP 2601 A 1 HETATM 20 N N7 GDP . . . E 2 275.501 244.956 332.706 1 77.12 ? N7 GDP 2601 A 1 HETATM 21 C C5 GDP . . . E 2 275.018 244.85 333.954 1 77.12 ? C5 GDP 2601 A 1 HETATM 22 C C6 GDP . . . E 2 275.049 243.826 335.021 1 77.12 ? C6 GDP 2601 A 1 HETATM 23 O O6 GDP . . . E 2 275.64 242.74 334.85 1 77.12 ? O6 GDP 2601 A 1 HETATM 24 N N1 GDP . . . E 2 274.428 244.099 336.171 1 77.12 ? N1 GDP 2601 A 1 HETATM 25 C C2 GDP . . . E 2 273.788 245.262 336.379 1 77.12 ? C2 GDP 2601 A 1 HETATM 26 N N2 GDP . . . E 2 273.183 245.46 337.574 1 77.12 ? N2 GDP 2601 A 1 HETATM 27 N N3 GDP . . . E 2 273.718 246.246 335.446 1 77.12 ? N3 GDP 2601 A 1 HETATM 28 C C4 GDP . . . E 2 274.307 246.102 334.238 1 77.12 ? C4 GDP 2601 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #