data_3K4Y # _model_server_result.job_id yz-IPII7LI0cRSMQ5n_CrA _model_server_result.datetime_utc '2025-02-23 16:16:58' _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 3k4y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":300}' # _entry.id 3K4Y # _exptl.entry_id 3K4Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-METHYLBUT-3-ENYL TRIHYDROGEN 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 90 _cell.angle_gamma 90 _cell.entry_id 3K4Y _cell.length_a 78.09 _cell.length_b 99.23 _cell.length_c 87.41 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K4Y _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 78.09 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 H12 O7 P2' _chem_comp.formula_weight 246.092 _chem_comp.id IPE _chem_comp.mon_nstd_flag . _chem_comp.name '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ISOPENTENYL PYROPHOSPHATE' # 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 C1 O1 IPE sing 173 n n C1 C2 IPE sing 174 n n C1 H11 IPE sing 175 n n C1 H12 IPE sing 176 n n O1 PA IPE sing 177 n n C2 C3 IPE sing 178 n n C2 H21 IPE sing 179 n n C2 H22 IPE sing 180 n n C3 C4 IPE doub 181 n n C3 C5 IPE sing 182 n n C4 H41 IPE sing 183 n n C4 H42 IPE sing 184 n n C5 H51 IPE sing 185 n n C5 H52 IPE sing 186 n n C5 H53 IPE sing 187 n n PA O1A IPE doub 188 n n PA O2A IPE sing 189 n n PA O3A IPE sing 190 n n O2A H2A IPE sing 191 n n O3A PB IPE sing 192 n n PB O1B IPE sing 193 n n PB O2B IPE doub 194 n n PB O3B IPE sing 195 n n O1B H1B IPE sing 196 n n O3B H3B IPE sing 197 n n # _atom_sites.entry_id 3K4Y _atom_sites.fract_transf_matrix[1][1] 0.012806 _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] 0.010078 _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] 0.01144 _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 IPE A 1 300 300 IPE IPE . D 3 SO4 A 1 262 262 SO4 SO4 . E 3 SO4 A 1 263 263 SO4 SO4 . F 2 IPE B 1 300 300 IPE IPE . G 3 SO4 B 1 262 262 SO4 SO4 . H 3 SO4 B 1 263 263 SO4 SO4 . I 4 HOH A 1 264 264 HOH HOH . I 4 HOH A 2 265 265 HOH HOH . I 4 HOH A 3 266 266 HOH HOH . I 4 HOH A 4 267 267 HOH HOH . I 4 HOH A 5 268 268 HOH HOH . I 4 HOH A 6 269 269 HOH HOH . I 4 HOH A 7 270 270 HOH HOH . I 4 HOH A 8 271 271 HOH HOH . I 4 HOH A 9 272 272 HOH HOH . I 4 HOH A 10 273 273 HOH HOH . I 4 HOH A 11 274 274 HOH HOH . I 4 HOH A 12 275 275 HOH HOH . I 4 HOH A 13 276 276 HOH HOH . I 4 HOH A 14 277 277 HOH HOH . I 4 HOH A 15 278 278 HOH HOH . I 4 HOH A 16 279 279 HOH HOH . I 4 HOH A 17 280 280 HOH HOH . I 4 HOH A 18 281 281 HOH HOH . I 4 HOH A 19 282 282 HOH HOH . I 4 HOH A 20 283 283 HOH HOH . I 4 HOH A 21 284 284 HOH HOH . I 4 HOH A 22 285 285 HOH HOH . I 4 HOH A 23 286 286 HOH HOH . I 4 HOH A 24 287 287 HOH HOH . I 4 HOH A 25 288 288 HOH HOH . I 4 HOH A 26 289 289 HOH HOH . I 4 HOH A 27 290 290 HOH HOH . I 4 HOH A 28 291 291 HOH HOH . I 4 HOH A 29 292 292 HOH HOH . I 4 HOH A 30 293 293 HOH HOH . I 4 HOH A 31 294 294 HOH HOH . I 4 HOH A 32 295 295 HOH HOH . I 4 HOH A 33 296 296 HOH HOH . I 4 HOH A 34 297 297 HOH HOH . I 4 HOH A 35 298 298 HOH HOH . I 4 HOH A 36 299 299 HOH HOH . I 4 HOH A 37 301 301 HOH HOH . I 4 HOH A 38 302 302 HOH HOH . I 4 HOH A 39 303 303 HOH HOH . I 4 HOH A 40 304 304 HOH HOH . I 4 HOH A 41 305 305 HOH HOH . I 4 HOH A 42 306 306 HOH HOH . I 4 HOH A 43 307 307 HOH HOH . I 4 HOH A 44 308 308 HOH HOH . I 4 HOH A 45 309 309 HOH HOH . I 4 HOH A 46 310 310 HOH HOH . I 4 HOH A 47 311 311 HOH HOH . I 4 HOH A 48 312 312 HOH HOH . I 4 HOH A 49 313 313 HOH HOH . I 4 HOH A 50 314 314 HOH HOH . I 4 HOH A 51 315 315 HOH HOH . I 4 HOH A 52 316 316 HOH HOH . I 4 HOH A 53 317 317 HOH HOH . I 4 HOH A 54 318 318 HOH HOH . I 4 HOH A 55 319 319 HOH HOH . I 4 HOH A 56 320 320 HOH HOH . I 4 HOH A 57 321 321 HOH HOH . I 4 HOH A 58 322 322 HOH HOH . I 4 HOH A 59 323 323 HOH HOH . I 4 HOH A 60 324 324 HOH HOH . J 4 HOH B 1 264 264 HOH HOH . J 4 HOH B 2 265 265 HOH HOH . J 4 HOH B 3 266 266 HOH HOH . J 4 HOH B 4 267 267 HOH HOH . J 4 HOH B 5 268 268 HOH HOH . J 4 HOH B 6 269 269 HOH HOH . J 4 HOH B 7 270 270 HOH HOH . J 4 HOH B 8 271 271 HOH HOH . J 4 HOH B 9 272 272 HOH HOH . J 4 HOH B 10 273 273 HOH HOH . J 4 HOH B 11 274 274 HOH HOH . J 4 HOH B 12 275 275 HOH HOH . J 4 HOH B 13 276 276 HOH HOH . J 4 HOH B 14 277 277 HOH HOH . J 4 HOH B 15 278 278 HOH HOH . J 4 HOH B 16 279 279 HOH HOH . J 4 HOH B 17 280 280 HOH HOH . J 4 HOH B 18 281 281 HOH HOH . J 4 HOH B 19 282 282 HOH HOH . J 4 HOH B 20 283 283 HOH HOH . J 4 HOH B 21 284 284 HOH HOH . J 4 HOH B 22 285 285 HOH HOH . J 4 HOH B 23 286 286 HOH HOH . J 4 HOH B 24 287 287 HOH HOH . J 4 HOH B 25 288 288 HOH HOH . J 4 HOH B 26 289 289 HOH HOH . J 4 HOH B 27 290 290 HOH HOH . J 4 HOH B 28 291 291 HOH HOH . J 4 HOH B 29 292 292 HOH HOH . J 4 HOH B 30 293 293 HOH HOH . J 4 HOH B 31 294 294 HOH HOH . J 4 HOH B 32 295 295 HOH HOH . J 4 HOH B 33 296 296 HOH HOH . J 4 HOH B 34 297 297 HOH HOH . J 4 HOH B 35 298 298 HOH HOH . J 4 HOH B 36 299 299 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 C C1 IPE . A . F 2 29.914 19.872 32.076 0.5 32.54 ? C1 IPE 300 B 1 HETATM 2 C C1 IPE . B . F 2 30.192 18.982 32.504 0.5 54.27 ? C1 IPE 300 B 1 HETATM 3 O O1 IPE . A . F 2 28.612 19.655 32.619 0.5 33.15 ? O1 IPE 300 B 1 HETATM 4 O O1 IPE . B . F 2 28.901 19.224 31.907 0.5 54.42 ? O1 IPE 300 B 1 HETATM 5 C C2 IPE . A . F 2 30.29 18.711 31.156 0.5 32.2 ? C2 IPE 300 B 1 HETATM 6 C C2 IPE . B . F 2 30.984 17.991 31.626 0.5 54.24 ? C2 IPE 300 B 1 HETATM 7 C C3 IPE . A . F 2 31.057 17.649 31.92 0.5 31.99 ? C3 IPE 300 B 1 HETATM 8 C C3 IPE . B . F 2 31.297 16.729 32.402 0.5 54.1 ? C3 IPE 300 B 1 HETATM 9 C C4 IPE . A . F 2 30.592 17.188 33.067 0.5 31.93 ? C4 IPE 300 B 1 HETATM 10 C C4 IPE . B . F 2 30.387 16.205 33.208 0.5 53.98 ? C4 IPE 300 B 1 HETATM 11 C C5 IPE . A . F 2 32.347 17.108 31.37 0.5 31.35 ? C5 IPE 300 B 1 HETATM 12 C C5 IPE . B . F 2 32.645 16.068 32.253 0.5 53.91 ? C5 IPE 300 B 1 HETATM 13 P PA IPE . A . F 2 27.348 20.54 32.147 0.5 34.1 ? PA IPE 300 B 1 HETATM 14 P PA IPE . B . F 2 28.226 20.687 31.969 0.5 54.57 ? PA IPE 300 B 1 HETATM 15 O O1A IPE . A . F 2 26.638 19.894 31.019 0.5 33.9 ? O1A IPE 300 B 1 HETATM 16 O O1A IPE . B . F 2 28.95 21.634 31.092 0.5 54.61 ? O1A IPE 300 B 1 HETATM 17 O O2A IPE . A . F 2 27.798 22.029 31.729 0.5 33.44 ? O2A IPE 300 B 1 HETATM 18 O O2A IPE . B . F 2 28.211 21.228 33.487 0.5 54.53 ? O2A IPE 300 B 1 HETATM 19 O O3A IPE . A . F 2 26.4 20.555 33.454 0.5 34.65 ? O3A IPE 300 B 1 HETATM 20 O O3A IPE . B . F 2 26.725 20.462 31.414 0.5 54.64 ? O3A IPE 300 B 1 HETATM 21 P PB IPE . A . F 2 26.989 20.867 34.922 0.5 34.9 ? PB IPE 300 B 1 HETATM 22 P PB IPE . B . F 2 25.593 19.731 32.303 0.5 54.71 ? PB IPE 300 B 1 HETATM 23 O O1B IPE . A . F 2 25.9 21.734 35.73 0.5 35.09 ? O1B IPE 300 B 1 HETATM 24 O O1B IPE . B . F 2 24.493 20.812 32.773 0.5 54.74 ? O1B IPE 300 B 1 HETATM 25 O O2B IPE . A . F 2 27.256 19.597 35.635 0.5 34.58 ? O2B IPE 300 B 1 HETATM 26 O O2B IPE . B . F 2 24.932 18.672 31.5 0.5 54.7 ? O2B IPE 300 B 1 HETATM 27 O O3B IPE . A . F 2 28.354 21.71 34.794 0.5 34.68 ? O3B IPE 300 B 1 HETATM 28 O O3B IPE . B . F 2 26.278 19.077 33.605 0.5 54.5 ? O3B IPE 300 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 566 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #