data_3WGL # _model_server_result.job_id rRS8tFNepRrD2dhL8KcBww _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":"C","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 . . . C 2 20.986 3.654 3.93 1 22.18 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . C 2 22.002 3.178 4.94 1 34.89 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . C 2 20.736 5.123 4.153 1 30.53 1 O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . C 2 19.71 2.878 4.109 1 23.79 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . C 2 21.604 3.438 2.462 1 34.6 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . C 2 20.712 2.943 1.219 1 30.01 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . C 2 19.389 3.668 1.214 1 32.68 1 O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . C 2 21.434 3.166 -0.089 1 30.53 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . C 2 20.521 1.368 1.483 1 27.72 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . C 2 21.245 0.437 0.69 1 30.99 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . C 2 20.336 -0.664 0.17 1 26.47 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . C 2 19.252 -0.052 -0.528 1 27.96 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . C 2 21.1 -1.508 -0.833 1 24.98 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . C 2 21.258 -2.844 -0.349 1 29.85 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . C 2 20.313 -1.461 -2.134 1 22.76 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . C 2 19.803 -2.749 -2.489 1 24.3 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . C 2 19.161 -0.506 -1.884 1 25.91 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . C 2 19.275 0.671 -2.783 1 25.34 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . C 2 20.373 1.424 -2.991 1 28.03 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . C 2 20.119 2.436 -3.86 1 25.54 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . C 2 18.828 2.346 -4.218 1 28.43 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . C 2 17.903 3.096 -5.102 1 30.37 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . C 2 18.287 4.095 -5.75 1 26.06 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . C 2 16.638 2.665 -5.186 1 30.26 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . C 2 16.195 1.591 -4.501 1 31.85 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . C 2 14.903 1.209 -4.631 1 35.5 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . C 2 16.985 0.862 -3.678 1 36.26 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . C 2 18.281 1.187 -3.5 1 29.89 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #