data_3WGL # _model_server_result.job_id rPG9Aoi2uUm2isDyqt97CA _model_server_result.datetime_utc '2024-11-05 00:56:40' _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 3wgl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 3WGL # _exptl.entry_id 3WGL _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.41 _cell.angle_gamma 90 _cell.entry_id 3WGL _cell.length_a 44.886 _cell.length_b 97.156 _cell.length_c 72.559 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WGL _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C 1 1 B,D 2 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 ? 2 C N N ? 2 D 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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 3WGL _atom_sites.fract_transf_matrix[1][1] 0.022279 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004904 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010293 _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] 0.014112 _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 A 1 401 1 GDP GDP . D 2 GDP B 1 401 1 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 . . . D 2 -25.425 27.103 -28.325 1 42.39 ? PB GDP 401 B 1 HETATM 2 O O1B GDP . . . D 2 -24.987 26.909 -26.894 1 41.35 ? O1B GDP 401 B 1 HETATM 3 O O2B GDP . . . D 2 -26.494 28.169 -28.387 1 50 1 O2B GDP 401 B 1 HETATM 4 O O3B GDP . . . D 2 -24.249 27.523 -29.174 1 41.72 ? O3B GDP 401 B 1 HETATM 5 O O3A GDP . . . D 2 -26.011 25.729 -28.911 1 45.32 ? O3A GDP 401 B 1 HETATM 6 P PA GDP . . . D 2 -25.365 24.298 -28.555 1 43.2 ? PA GDP 401 B 1 HETATM 7 O O1A GDP . . . D 2 -24.15 24.433 -27.671 1 37.67 1 O1A GDP 401 B 1 HETATM 8 O O2A GDP . . . D 2 -26.39 23.392 -27.914 1 43.9 ? O2A GDP 401 B 1 HETATM 9 O O5' GDP . . . D 2 -24.948 23.753 -30.008 1 40.14 ? O5' GDP 401 B 1 HETATM 10 C C5' GDP . . . D 2 -25.716 22.732 -30.624 1 36.67 ? C5' GDP 401 B 1 HETATM 11 C C4' GDP . . . D 2 -24.82 21.791 -31.405 1 36.63 ? C4' GDP 401 B 1 HETATM 12 O O4' GDP . . . D 2 -23.727 21.417 -30.567 1 40.73 ? O4' GDP 401 B 1 HETATM 13 C C3' GDP . . . D 2 -25.587 20.525 -31.727 1 35.81 ? C3' GDP 401 B 1 HETATM 14 O O3' GDP . . . D 2 -25.898 20.471 -33.123 1 40.04 ? O3' GDP 401 B 1 HETATM 15 C C2' GDP . . . D 2 -24.686 19.377 -31.319 1 33.78 ? C2' GDP 401 B 1 HETATM 16 O O2' GDP . . . D 2 -24.124 18.769 -32.485 1 35.75 ? O2' GDP 401 B 1 HETATM 17 C C1' GDP . . . D 2 -23.58 19.996 -30.483 1 37.4 ? C1' GDP 401 B 1 HETATM 18 N N9 GDP . . . D 2 -23.699 19.578 -29.058 1 38.13 ? N9 GDP 401 B 1 HETATM 19 C C8 GDP . . . D 2 -24.793 19.692 -28.28 1 38.79 ? C8 GDP 401 B 1 HETATM 20 N N7 GDP . . . D 2 -24.559 19.226 -27.026 1 38.18 ? N7 GDP 401 B 1 HETATM 21 C C5 GDP . . . D 2 -23.281 18.808 -26.977 1 40.36 ? C5 GDP 401 B 1 HETATM 22 C C6 GDP . . . D 2 -22.382 18.208 -25.956 1 42.79 ? C6 GDP 401 B 1 HETATM 23 O O6 GDP . . . D 2 -22.764 17.969 -24.789 1 33.01 ? O6 GDP 401 B 1 HETATM 24 N N1 GDP . . . D 2 -21.128 17.926 -26.325 1 50.75 ? N1 GDP 401 B 1 HETATM 25 C C2 GDP . . . D 2 -20.671 18.168 -27.569 1 48.79 ? C2 GDP 401 B 1 HETATM 26 N N2 GDP . . . D 2 -19.385 17.851 -27.852 1 47.23 ? N2 GDP 401 B 1 HETATM 27 N N3 GDP . . . D 2 -21.435 18.712 -28.55 1 45.05 ? N3 GDP 401 B 1 HETATM 28 C C4 GDP . . . D 2 -22.723 19.048 -28.318 1 40.37 ? C4 GDP 401 B 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 213 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #