data_8R9R # _model_server_result.job_id qmZztebXTz8ryY83aGZkCA _model_server_result.datetime_utc '2024-10-18 17:24:26' _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 8r9r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8R9R # _exptl.entry_id 8R9R _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 120 _cell.entry_id 8R9R _cell.length_a 73.92 _cell.length_b 73.92 _cell.length_c 159.96 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8R9R _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 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' 8_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 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 8R9R _atom_sites.fract_transf_matrix[1][1] 0.013528 _atom_sites.fract_transf_matrix[1][2] 0.00781 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015621 _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] 0.006252 _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 1 501 1 GDP GDP . C 3 HOH A 1 601 1 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 -23.121 3.658 2.897 1 62.55 ? PB GDP 501 A 1 HETATM 2 O O1B GDP . . . B 2 -22.82 2.188 3.041 1 65.99 ? O1B GDP 501 A 1 HETATM 3 O O2B GDP . . . B 2 -24.258 4.081 3.77 1 62.21 ? O2B GDP 501 A 1 HETATM 4 O O3B GDP . . . B 2 -21.964 4.532 3.234 1 66.56 ? O3B GDP 501 A 1 HETATM 5 O O3A GDP . . . B 2 -23.467 3.864 1.333 1 61.4 ? O3A GDP 501 A 1 HETATM 6 P PA GDP . . . B 2 -22.263 4.3 0.295 1 63.14 ? PA GDP 501 A 1 HETATM 7 O O1A GDP . . . B 2 -21.968 5.809 0.441 1 65.95 ? O1A GDP 501 A 1 HETATM 8 O O2A GDP . . . B 2 -21.023 3.449 0.566 1 68.91 ? O2A GDP 501 A 1 HETATM 9 O O5' GDP . . . B 2 -22.87 3.999 -1.187 1 58.34 ? O5' GDP 501 A 1 HETATM 10 C C5' GDP . . . B 2 -23.675 2.887 -1.259 1 58.99 ? C5' GDP 501 A 1 HETATM 11 C C4' GDP . . . B 2 -23.96 2.601 -2.714 1 60 ? C4' GDP 501 A 1 HETATM 12 O O4' GDP . . . B 2 -25.24 3.532 -3.047 1 60.4 ? O4' GDP 501 A 1 HETATM 13 C C3' GDP . . . B 2 -22.992 2.945 -3.527 1 58.02 ? C3' GDP 501 A 1 HETATM 14 O O3' GDP . . . B 2 -23.023 2.093 -4.726 1 58.5 ? O3' GDP 501 A 1 HETATM 15 C C2' GDP . . . B 2 -23.329 4.409 -3.99 1 59.14 ? C2' GDP 501 A 1 HETATM 16 O O2' GDP . . . B 2 -22.829 4.659 -5.223 1 59.01 ? O2' GDP 501 A 1 HETATM 17 C C1' GDP . . . B 2 -24.848 4.285 -4.076 1 61.02 ? C1' GDP 501 A 1 HETATM 18 N N9 GDP . . . B 2 -25.591 5.579 -4.056 1 59.78 ? N9 GDP 501 A 1 HETATM 19 C C8 GDP . . . B 2 -25.351 6.421 -3.034 1 58.49 ? C8 GDP 501 A 1 HETATM 20 N N7 GDP . . . B 2 -26.158 7.494 -3.243 1 58.33 ? N7 GDP 501 A 1 HETATM 21 C C5 GDP . . . B 2 -26.862 7.274 -4.364 1 58.49 ? C5 GDP 501 A 1 HETATM 22 C C6 GDP . . . B 2 -27.913 8.046 -5.144 1 57.21 ? C6 GDP 501 A 1 HETATM 23 O O6 GDP . . . B 2 -28.278 9.111 -4.79 1 59.53 ? O6 GDP 501 A 1 HETATM 24 N N1 GDP . . . B 2 -28.461 7.457 -6.343 1 55.37 ? N1 GDP 501 A 1 HETATM 25 C C2 GDP . . . B 2 -28.023 6.169 -6.791 1 54.54 ? C2 GDP 501 A 1 HETATM 26 N N2 GDP . . . B 2 -28.522 5.491 -8.008 1 57.08 ? N2 GDP 501 A 1 HETATM 27 N N3 GDP . . . B 2 -27.049 5.446 -6.062 1 58.37 ? N3 GDP 501 A 1 HETATM 28 C C4 GDP . . . B 2 -26.489 6.075 -4.841 1 58.96 ? C4 GDP 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #