data_1WKK # _model_server_result.job_id 4CbeOP46sKgNnk6gC-8Fgg _model_server_result.datetime_utc '2024-12-26 19:40:12' _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 1wkk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 1WKK # _exptl.entry_id 1WKK _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 1WKK _cell.length_a 123.83 _cell.length_b 123.83 _cell.length_c 104.302 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WKK _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 61.915 107.239926 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -61.915 107.239926 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 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 1WKK _atom_sites.fract_transf_matrix[1][1] 0.008076 _atom_sites.fract_transf_matrix[1][2] 0.004662 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009325 _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] 0.009588 _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 1001 1 GDP GDP . D 3 HOH A 1 1002 3 HOH TIP . D 3 HOH A 2 1003 9 HOH TIP . D 3 HOH A 3 1004 10 HOH TIP . D 3 HOH A 4 1005 13 HOH TIP . D 3 HOH A 5 1006 14 HOH TIP . D 3 HOH A 6 1007 17 HOH TIP . D 3 HOH A 7 1008 18 HOH TIP . D 3 HOH A 8 1009 22 HOH TIP . D 3 HOH A 9 1010 24 HOH TIP . D 3 HOH A 10 1011 25 HOH TIP . D 3 HOH A 11 1012 26 HOH TIP . D 3 HOH A 12 1013 27 HOH TIP . D 3 HOH A 13 1014 28 HOH TIP . D 3 HOH A 14 1015 29 HOH TIP . D 3 HOH A 15 1016 30 HOH TIP . D 3 HOH A 16 1017 31 HOH TIP . D 3 HOH A 17 1018 33 HOH TIP . D 3 HOH A 18 1019 36 HOH TIP . D 3 HOH A 19 1020 39 HOH TIP . D 3 HOH A 20 1021 43 HOH TIP . D 3 HOH A 21 1022 44 HOH TIP . D 3 HOH A 22 1023 45 HOH TIP . D 3 HOH A 23 1024 46 HOH TIP . D 3 HOH A 24 1025 48 HOH TIP . E 3 HOH B 1 138 1 HOH TIP . E 3 HOH B 2 139 2 HOH TIP . E 3 HOH B 3 140 4 HOH TIP . E 3 HOH B 4 141 5 HOH TIP . E 3 HOH B 5 142 6 HOH TIP . E 3 HOH B 6 143 7 HOH TIP . E 3 HOH B 7 144 8 HOH TIP . E 3 HOH B 8 145 11 HOH TIP . E 3 HOH B 9 146 12 HOH TIP . E 3 HOH B 10 147 15 HOH TIP . E 3 HOH B 11 148 16 HOH TIP . E 3 HOH B 12 149 19 HOH TIP . E 3 HOH B 13 150 20 HOH TIP . E 3 HOH B 14 151 21 HOH TIP . E 3 HOH B 15 152 23 HOH TIP . E 3 HOH B 16 153 32 HOH TIP . E 3 HOH B 17 154 34 HOH TIP . E 3 HOH B 18 155 35 HOH TIP . E 3 HOH B 19 156 37 HOH TIP . E 3 HOH B 20 157 38 HOH TIP . E 3 HOH B 21 158 40 HOH TIP . E 3 HOH B 22 159 41 HOH TIP . E 3 HOH B 23 160 42 HOH TIP . E 3 HOH B 24 161 47 HOH TIP . E 3 HOH B 25 162 49 HOH TIP . # 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 17.729 62.945 34.97 0.49 45 ? PB GDP 1001 A 1 HETATM 2 O O1B GDP . . . C 2 17.413 62.545 36.369 0.49 43.99 ? O1B GDP 1001 A 1 HETATM 3 O O2B GDP . . . C 2 17.93 64.443 34.799 0.49 43.51 ? O2B GDP 1001 A 1 HETATM 4 O O3B GDP . . . C 2 16.712 62.379 33.946 0.49 41.61 ? O3B GDP 1001 A 1 HETATM 5 O O3A GDP . . . C 2 19.196 62.241 34.605 0.49 47.19 ? O3A GDP 1001 A 1 HETATM 6 P PA GDP . . . C 2 19.605 61.417 33.333 0.49 50.15 ? PA GDP 1001 A 1 HETATM 7 O O1A GDP . . . C 2 18.748 61.765 32.169 0.49 50.82 ? O1A GDP 1001 A 1 HETATM 8 O O2A GDP . . . C 2 19.658 59.928 33.672 0.49 51 ? O2A GDP 1001 A 1 HETATM 9 O O5' GDP . . . C 2 21.12 61.878 33.058 0.49 49.41 ? O5' GDP 1001 A 1 HETATM 10 C C5' GDP . . . C 2 21.413 63.229 32.711 0.49 48.34 ? C5' GDP 1001 A 1 HETATM 11 C C4' GDP . . . C 2 22.161 63.825 33.86 0.49 48.1 ? C4' GDP 1001 A 1 HETATM 12 O O4' GDP . . . C 2 23.148 64.726 33.272 0.49 48.41 ? O4' GDP 1001 A 1 HETATM 13 C C3' GDP . . . C 2 21.276 64.64 34.819 0.49 47.8 ? C3' GDP 1001 A 1 HETATM 14 O O3' GDP . . . C 2 21.836 64.376 36.155 0.49 49.27 ? O3' GDP 1001 A 1 HETATM 15 C C2' GDP . . . C 2 21.512 66.071 34.397 0.49 47.79 ? C2' GDP 1001 A 1 HETATM 16 O O2' GDP . . . C 2 21.302 66.975 35.452 0.49 46.29 ? O2' GDP 1001 A 1 HETATM 17 C C1' GDP . . . C 2 22.939 66.02 33.777 0.49 47.84 ? C1' GDP 1001 A 1 HETATM 18 N N9 GDP . . . C 2 23.063 67.05 32.598 0.49 47.97 ? N9 GDP 1001 A 1 HETATM 19 C C8 GDP . . . C 2 23.01 66.756 31.258 0.49 47.38 ? C8 GDP 1001 A 1 HETATM 20 N N7 GDP . . . C 2 23.149 67.876 30.529 0.49 48.05 ? N7 GDP 1001 A 1 HETATM 21 C C5 GDP . . . C 2 23.294 68.907 31.461 0.49 48.25 ? C5 GDP 1001 A 1 HETATM 22 C C6 GDP . . . C 2 23.474 70.302 31.266 0.49 49.04 ? C6 GDP 1001 A 1 HETATM 23 O O6 GDP . . . C 2 23.537 70.886 30.167 0.49 50.03 ? O6 GDP 1001 A 1 HETATM 24 N N1 GDP . . . C 2 23.581 71.03 32.473 0.49 50.15 ? N1 GDP 1001 A 1 HETATM 25 C C2 GDP . . . C 2 23.516 70.425 33.73 0.49 50.24 ? C2 GDP 1001 A 1 HETATM 26 N N2 GDP . . . C 2 23.628 71.211 34.81 0.49 49.54 ? N2 GDP 1001 A 1 HETATM 27 N N3 GDP . . . C 2 23.344 69.095 33.91 0.49 48.68 ? N3 GDP 1001 A 1 HETATM 28 C C4 GDP . . . C 2 23.243 68.41 32.738 0.49 48.15 ? C4 GDP 1001 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #