data_4PDE # _model_server_result.job_id GfTseopHS5PXx1bYsaDolg _model_server_result.datetime_utc '2024-11-17 07:37:50' _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 4pde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 4PDE # _exptl.entry_id 4PDE _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 4PDE _cell.length_a 98.43 _cell.length_b 98.43 _cell.length_c 120.411 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PDE _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 PISA _pdbx_struct_assembly.oligomeric_details Dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -49.215 85.24288 20.0685 # _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 4PDE _atom_sites.fract_transf_matrix[1][1] 0.01016 _atom_sites.fract_transf_matrix[1][2] 0.005866 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011731 _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] 0.008305 _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 1 300 300 GDP GDP . C 3 HOH A 1 401 16 HOH HOH . C 3 HOH A 2 402 8 HOH HOH . C 3 HOH A 3 403 1 HOH HOH . C 3 HOH A 4 404 3 HOH HOH . C 3 HOH A 5 405 2 HOH HOH . C 3 HOH A 6 406 4 HOH HOH . C 3 HOH A 7 407 5 HOH HOH . C 3 HOH A 8 408 6 HOH HOH . C 3 HOH A 9 409 7 HOH HOH . C 3 HOH A 10 410 9 HOH HOH . C 3 HOH A 11 411 10 HOH HOH . C 3 HOH A 12 412 11 HOH HOH . C 3 HOH A 13 413 12 HOH HOH . C 3 HOH A 14 414 13 HOH HOH . C 3 HOH A 15 415 14 HOH HOH . C 3 HOH A 16 416 15 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 -26.742 43.384 7.815 1 122.76 ? PB GDP 300 A 1 HETATM 2 O O1B GDP . . . B 2 -27.219 42.093 7.18 1 116.79 ? O1B GDP 300 A 1 HETATM 3 O O2B GDP . . . B 2 -26.5 43.207 9.294 1 123.78 ? O2B GDP 300 A 1 HETATM 4 O O3B GDP . . . B 2 -27.813 44.433 7.634 1 123.38 ? O3B GDP 300 A 1 HETATM 5 O O3A GDP . . . B 2 -25.37 43.881 7.124 1 62.58 ? O3A GDP 300 A 1 HETATM 6 P PA GDP . . . B 2 -25.38 44.1 5.535 1 110.56 ? PA GDP 300 A 1 HETATM 7 O O1A GDP . . . B 2 -24.003 43.941 4.938 1 109.16 ? O1A GDP 300 A 1 HETATM 8 O O2A GDP . . . B 2 -26.389 43.175 4.894 1 113.5 ? O2A GDP 300 A 1 HETATM 9 O O5' GDP . . . B 2 -25.877 45.615 5.396 1 73.35 ? O5' GDP 300 A 1 HETATM 10 C C5' GDP . . . B 2 -26.793 45.899 4.355 1 73.52 ? C5' GDP 300 A 1 HETATM 11 C C4' GDP . . . B 2 -27.701 47.038 4.76 1 76.12 ? C4' GDP 300 A 1 HETATM 12 O O4' GDP . . . B 2 -27.74 47.923 3.65 1 78.06 ? O4' GDP 300 A 1 HETATM 13 C C3' GDP . . . B 2 -29.113 46.541 5.008 1 83.3 ? C3' GDP 300 A 1 HETATM 14 O O3' GDP . . . B 2 -29.524 46.917 6.327 1 96.05 ? O3' GDP 300 A 1 HETATM 15 C C2' GDP . . . B 2 -29.986 47.219 3.97 1 77.44 ? C2' GDP 300 A 1 HETATM 16 O O2' GDP . . . B 2 -30.881 48.153 4.58 1 76.38 ? O2' GDP 300 A 1 HETATM 17 C C1' GDP . . . B 2 -29.038 47.982 3.065 1 74.96 ? C1' GDP 300 A 1 HETATM 18 N N9 GDP . . . B 2 -28.984 47.337 1.729 1 63.82 ? N9 GDP 300 A 1 HETATM 19 C C8 GDP . . . B 2 -28.913 46.009 1.492 1 57.9 ? C8 GDP 300 A 1 HETATM 20 N N7 GDP . . . B 2 -28.873 45.743 0.164 1 51.9 ? N7 GDP 300 A 1 HETATM 21 C C5 GDP . . . B 2 -28.908 46.929 -0.469 1 51.03 ? C5 GDP 300 A 1 HETATM 22 C C6 GDP . . . B 2 -28.885 47.373 -1.874 1 44.65 ? C6 GDP 300 A 1 HETATM 23 O O6 GDP . . . B 2 -28.824 46.551 -2.813 1 39.63 ? O6 GDP 300 A 1 HETATM 24 N N1 GDP . . . B 2 -28.935 48.692 -2.096 1 48.22 ? N1 GDP 300 A 1 HETATM 25 C C2 GDP . . . B 2 -28.998 49.613 -1.117 1 45.69 ? C2 GDP 300 A 1 HETATM 26 N N2 GDP . . . B 2 -29.04 50.918 -1.474 1 43.4 ? N2 GDP 300 A 1 HETATM 27 N N3 GDP . . . B 2 -29.022 49.284 0.197 1 47.87 ? N3 GDP 300 A 1 HETATM 28 C C4 GDP . . . B 2 -28.978 47.98 0.564 1 55.16 ? C4 GDP 300 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #