data_5OXF # _model_server_result.job_id GbZ0gcURmFfkqikFbLEN7g _model_server_result.datetime_utc '2024-11-22 18:58:46' _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 5oxf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1000}' # _entry.id 5OXF # _exptl.entry_id 5OXF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 5OXF _cell.length_a 114.717 _cell.length_b 228.675 _cell.length_c 318.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OXF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H 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 5OXF _atom_sites.fract_transf_matrix[1][1] 0.008717 _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] 0.004373 _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] 0.003137 _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 E 3 GDP A 1 1000 1000 GDP GDP . F 3 GDP B 1 1000 1000 GDP GDP . G 3 GDP C 1 1000 1000 GDP GDP . H 3 GDP D 1 1000 1000 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 . . . E 3 -2.003 76.844 -54.976 1 199.84 ? PB GDP 1000 A 1 HETATM 2 O O1B GDP . . . E 3 -1.246 77.971 -55.635 1 214.32 ? O1B GDP 1000 A 1 HETATM 3 O O2B GDP . . . E 3 -3.494 77.048 -55.109 1 212.14 -1 O2B GDP 1000 A 1 HETATM 4 O O3B GDP . . . E 3 -1.609 75.531 -55.604 1 212.53 ? O3B GDP 1000 A 1 HETATM 5 O O3A GDP . . . E 3 -1.628 76.823 -53.41 1 180.21 ? O3A GDP 1000 A 1 HETATM 6 P PA GDP . . . E 3 -1.958 78.097 -52.483 1 249.08 ? PA GDP 1000 A 1 HETATM 7 O O1A GDP . . . E 3 -2.739 79.098 -53.299 1 319.45 ? O1A GDP 1000 A 1 HETATM 8 O O2A GDP . . . E 3 -0.667 78.721 -52.008 1 245.72 -1 O2A GDP 1000 A 1 HETATM 9 O O5' GDP . . . E 3 -2.86 77.647 -51.223 1 249.99 ? O5' GDP 1000 A 1 HETATM 10 C C5' GDP . . . E 3 -4.283 77.582 -51.338 1 256.84 ? C5' GDP 1000 A 1 HETATM 11 C C4' GDP . . . E 3 -4.948 78.105 -50.066 1 261.62 ? C4' GDP 1000 A 1 HETATM 12 O O4' GDP . . . E 3 -4.679 77.22 -48.976 1 242.37 ? O4' GDP 1000 A 1 HETATM 13 C C3' GDP . . . E 3 -4.428 79.475 -49.661 1 289.06 ? C3' GDP 1000 A 1 HETATM 14 O O3' GDP . . . E 3 -5.525 80.298 -49.258 1 315.28 ? O3' GDP 1000 A 1 HETATM 15 C C2' GDP . . . E 3 -3.526 79.223 -48.472 1 280.59 ? C2' GDP 1000 A 1 HETATM 16 O O2' GDP . . . E 3 -3.665 80.274 -47.512 1 330.06 ? O2' GDP 1000 A 1 HETATM 17 C C1' GDP . . . E 3 -4.019 77.902 -47.908 1 260.65 ? C1' GDP 1000 A 1 HETATM 18 N N9 GDP . . . E 3 -2.882 77.058 -47.484 1 261.8 ? N9 GDP 1000 A 1 HETATM 19 C C8 GDP . . . E 3 -1.84 76.739 -48.264 1 254.1 ? C8 GDP 1000 A 1 HETATM 20 N N7 GDP . . . E 3 -0.962 75.938 -47.61 1 258.05 ? N7 GDP 1000 A 1 HETATM 21 C C5 GDP . . . E 3 -1.456 75.728 -46.38 1 275.97 ? C5 GDP 1000 A 1 HETATM 22 C C6 GDP . . . E 3 -1.034 74.975 -45.18 1 287.45 ? C6 GDP 1000 A 1 HETATM 23 O O6 GDP . . . E 3 0.029 74.328 -45.175 1 295.49 ? O6 GDP 1000 A 1 HETATM 24 N N1 GDP . . . E 3 -1.826 75.004 -44.105 1 279.39 ? N1 GDP 1000 A 1 HETATM 25 C C2 GDP . . . E 3 -2.979 75.696 -44.084 1 268.15 ? C2 GDP 1000 A 1 HETATM 26 N N2 GDP . . . E 3 -3.726 75.679 -42.955 1 254.29 ? N2 GDP 1000 A 1 HETATM 27 N N3 GDP . . . E 3 -3.43 76.41 -45.148 1 284 ? N3 GDP 1000 A 1 HETATM 28 C C4 GDP . . . E 3 -2.725 76.462 -46.301 1 274.66 ? C4 GDP 1000 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #