data_8OY1 # _model_server_result.job_id 3lvJ9M6Z3Vnxtqw1lbcWGw _model_server_result.datetime_utc '2024-10-11 02:25:16' _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 8oy1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8OY1 # _exptl.entry_id 8OY1 _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 8OY1 _cell.length_a 113.065 _cell.length_b 113.065 _cell.length_c 68.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OY1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall 'P 4n 2n' _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 8OY1 _atom_sites.fract_transf_matrix[1][1] 0.008844 _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] 0.008844 _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] 0.01456 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GDP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _pdbx_nonpoly_scheme.pdb_mon_id GDP _pdbx_nonpoly_scheme.auth_mon_id GDP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 13.881 -29.699 -7.537 1 132.1 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 12.947 -28.679 -8.142 1 140.77 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 14.958 -28.978 -6.775 1 130.28 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 13.051 -30.558 -6.619 1 135.05 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 14.458 -30.578 -8.729 1 134.47 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 15.797 -31.401 -8.678 1 163.32 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 16.929 -30.669 -9.293 1 132.45 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 16.074 -31.898 -7.289 1 146.59 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 15.438 -32.558 -9.682 1 139.91 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 15.015 -33.77 -9.11 1 136.18 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 15.707 -34.901 -9.852 1 137.51 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 15.119 -34.889 -11.133 1 139.72 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 17.202 -34.636 -10.034 1 133.55 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 17.987 -35.83 -9.842 1 141.01 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 17.373 -34.273 -11.465 1 129.67 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 18.595 -34.906 -11.835 1 137.81 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 16.173 -34.981 -12.064 1 137.76 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 15.582 -34.451 -13.296 1 142.14 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 15.019 -33.258 -13.563 1 144.23 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 14.567 -33.236 -14.84 1 140.75 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 14.827 -34.454 -15.365 1 135.96 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 14.616 -35.144 -16.651 1 133.15 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 14.05 -34.514 -17.567 1 135.2 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 15.036 -36.42 -16.789 1 130.03 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 15.648 -37.091 -15.779 1 136.19 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 16.057 -38.382 -15.949 1 131.62 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 15.873 -36.527 -14.565 1 142.65 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 15.485 -35.248 -14.334 1 140.62 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #