data_3K56 # _model_server_result.job_id xnTDPKi73y5S_hbJZVqm_g _model_server_result.datetime_utc '2025-02-23 15:55:14' _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 3k56 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 3K56 # _exptl.entry_id 3K56 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 264.174 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Isopentenyl Diphosphate Beta-S' _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 90 _cell.angle_gamma 90 _cell.entry_id 3K56 _cell.length_a 77.68 _cell.length_b 100.24 _cell.length_c 87.79 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K56 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 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 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 77.68 0 0 2 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 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 F N N # _chem_comp.formula 'C5 H14 O6 P2 S' _chem_comp.formula_weight 264.174 _chem_comp.id IS3 _chem_comp.mon_nstd_flag . _chem_comp.name 'Isopentenyl Diphosphate Beta-S' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'O-(3-methylbutyl) trihydrogen thiodiphosphate' # 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 O P1 IS3 sing 173 n n O P2 IS3 sing 174 n n C1 O1 IS3 sing 175 n n C1 C2 IS3 sing 176 n n C1 H1 IS3 sing 177 n n C1 H1A IS3 sing 178 n n O1 P1 IS3 sing 179 n n P1 O2 IS3 sing 180 n n P1 O3 IS3 doub 181 n n C2 C3 IS3 sing 182 n n C2 H2 IS3 sing 183 n n C2 H2A IS3 sing 184 n n P2 O4 IS3 doub 185 n n P2 O5 IS3 sing 186 n n P2 S6 IS3 sing 187 n n C3 C4 IS3 sing 188 n n C3 C5 IS3 sing 189 n n C4 H4 IS3 sing 190 n n C4 H4A IS3 sing 191 n n C4 H4B IS3 sing 192 n n C5 H5 IS3 sing 193 n n C5 H5A IS3 sing 194 n n O2 H10 IS3 sing 195 n n C3 H11 IS3 sing 196 n n C5 H12 IS3 sing 197 n n O5 H13 IS3 sing 198 n n S6 H14 IS3 sing 199 n n # _atom_sites.entry_id 3K56 _atom_sites.fract_transf_matrix[1][1] 0.012873 _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] 0.009976 _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] 0.011391 _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 IS3 A 1 300 300 IS3 IS3 . D 3 SO4 A 1 303 303 SO4 SO4 . E 3 SO4 A 1 304 304 SO4 SO4 . F 2 IS3 B 1 300 300 IS3 IS3 . G 3 SO4 B 1 301 301 SO4 SO4 . H 3 SO4 B 1 302 302 SO4 SO4 . I 4 HOH A 1 261 261 HOH HOH . I 4 HOH A 2 262 262 HOH HOH . I 4 HOH A 3 263 263 HOH HOH . I 4 HOH A 4 264 264 HOH HOH . I 4 HOH A 5 265 265 HOH HOH . I 4 HOH A 6 266 266 HOH HOH . I 4 HOH A 7 267 267 HOH HOH . I 4 HOH A 8 268 268 HOH HOH . I 4 HOH A 9 269 269 HOH HOH . I 4 HOH A 10 270 270 HOH HOH . I 4 HOH A 11 271 271 HOH HOH . I 4 HOH A 12 272 272 HOH HOH . I 4 HOH A 13 273 273 HOH HOH . I 4 HOH A 14 274 274 HOH HOH . I 4 HOH A 15 275 275 HOH HOH . I 4 HOH A 16 276 276 HOH HOH . I 4 HOH A 17 277 277 HOH HOH . I 4 HOH A 18 278 278 HOH HOH . I 4 HOH A 19 279 279 HOH HOH . I 4 HOH A 20 280 280 HOH HOH . I 4 HOH A 21 281 281 HOH HOH . I 4 HOH A 22 282 282 HOH HOH . I 4 HOH A 23 283 283 HOH HOH . I 4 HOH A 24 284 284 HOH HOH . I 4 HOH A 25 285 285 HOH HOH . I 4 HOH A 26 286 286 HOH HOH . I 4 HOH A 27 287 287 HOH HOH . I 4 HOH A 28 288 288 HOH HOH . I 4 HOH A 29 289 289 HOH HOH . I 4 HOH A 30 290 290 HOH HOH . I 4 HOH A 31 291 291 HOH HOH . I 4 HOH A 32 292 292 HOH HOH . I 4 HOH A 33 293 293 HOH HOH . I 4 HOH A 34 294 294 HOH HOH . I 4 HOH A 35 295 295 HOH HOH . I 4 HOH A 36 296 296 HOH HOH . I 4 HOH A 37 297 297 HOH HOH . I 4 HOH A 38 298 298 HOH HOH . I 4 HOH A 39 299 299 HOH HOH . I 4 HOH A 40 301 301 HOH HOH . I 4 HOH A 41 302 302 HOH HOH . J 4 HOH B 1 261 261 HOH HOH . J 4 HOH B 2 262 262 HOH HOH . J 4 HOH B 3 263 263 HOH HOH . J 4 HOH B 4 264 264 HOH HOH . J 4 HOH B 5 265 265 HOH HOH . J 4 HOH B 6 266 266 HOH HOH . J 4 HOH B 7 267 267 HOH HOH . J 4 HOH B 8 268 268 HOH HOH . J 4 HOH B 9 269 269 HOH HOH . J 4 HOH B 10 270 270 HOH HOH . J 4 HOH B 11 271 271 HOH HOH . J 4 HOH B 12 272 272 HOH HOH . J 4 HOH B 13 273 273 HOH HOH . J 4 HOH B 14 274 274 HOH HOH . J 4 HOH B 15 275 275 HOH HOH . J 4 HOH B 16 276 276 HOH HOH . J 4 HOH B 17 277 277 HOH HOH . J 4 HOH B 18 279 279 HOH HOH . J 4 HOH B 19 280 280 HOH HOH . J 4 HOH B 20 281 281 HOH HOH . J 4 HOH B 21 282 282 HOH HOH . J 4 HOH B 22 283 283 HOH HOH . J 4 HOH B 23 284 284 HOH HOH . J 4 HOH B 24 285 285 HOH HOH . J 4 HOH B 25 286 286 HOH HOH . J 4 HOH B 26 287 287 HOH HOH . J 4 HOH B 27 288 288 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 O O IS3 . . . C 2 49.65 13.126 8.34 1 65.02 ? O IS3 300 A 1 HETATM 2 C C1 IS3 . . . C 2 47.545 14.985 9.008 1 61.69 ? C1 IS3 300 A 1 HETATM 3 O O1 IS3 . . . C 2 48.899 15.448 9.03 1 61.58 ? O1 IS3 300 A 1 HETATM 4 P P1 IS3 . . . C 2 50.238 14.551 8.851 1 61.26 ? P1 IS3 300 A 1 HETATM 5 C C2 IS3 . . . C 2 46.973 14.849 7.6 1 61.29 ? C2 IS3 300 A 1 HETATM 6 O O2 IS3 . . . C 2 50.948 14.451 10.182 1 63.23 ? O2 IS3 300 A 1 HETATM 7 P P2 IS3 . . . C 2 50.533 11.824 7.816 1 68.13 ? P2 IS3 300 A 1 HETATM 8 C C3 IS3 . . . C 2 45.553 15.403 7.45 1 63.27 ? C3 IS3 300 A 1 HETATM 9 O O3 IS3 . . . C 2 51.038 15.129 7.709 1 64.08 ? O3 IS3 300 A 1 HETATM 10 C C4 IS3 . . . C 2 44.84 15.256 6.125 1 61.4 ? C4 IS3 300 A 1 HETATM 11 O O4 IS3 . . . C 2 51.025 12.314 6.479 1 64.77 ? O4 IS3 300 A 1 HETATM 12 C C5 IS3 . . . C 2 44.907 16.001 8.446 1 60.3 ? C5 IS3 300 A 1 HETATM 13 O O5 IS3 . . . C 2 49.731 10.484 7.821 1 63.26 ? O5 IS3 300 A 1 HETATM 14 S S6 IS3 . . . C 2 52.036 11.498 9.135 1 71.45 ? S6 IS3 300 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #