data_6YPF # _model_server_result.job_id ixdzyNQqqt37u88IS3DhyQ _model_server_result.datetime_utc '2025-03-06 08:58:02' _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 6ypf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6YPF # _exptl.entry_id 6YPF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL 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 6YPF _cell.length_a 49.287 _cell.length_b 49.287 _cell.length_c 104.286 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YPF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _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 H20 O7 P2' _chem_comp.formula_weight 314.209 _chem_comp.id GPP _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL DIPHOSPHATE' _chem_comp.type non-polymer _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 C1 O1 GPP sing 129 n n C1 C2 GPP sing 130 n n C1 H11 GPP sing 131 n n C1 H12 GPP sing 132 n n O1 PA GPP sing 133 n n C2 C3 GPP doub 134 e n C2 H2 GPP sing 135 n n C3 C4 GPP sing 136 n n C3 C5 GPP sing 137 n n C4 H41 GPP sing 138 n n C4 H42 GPP sing 139 n n C4 H43 GPP sing 140 n n C5 C6 GPP sing 141 n n C5 H51 GPP sing 142 n n C5 H52 GPP sing 143 n n C6 C7 GPP sing 144 n n C6 H61 GPP sing 145 n n C6 H62 GPP sing 146 n n C7 C8 GPP doub 147 n n C7 H7 GPP sing 148 n n C8 C9 GPP sing 149 n n C8 C10 GPP sing 150 n n C9 H91 GPP sing 151 n n C9 H92 GPP sing 152 n n C9 H93 GPP sing 153 n n C10 H101 GPP sing 154 n n C10 H102 GPP sing 155 n n C10 H103 GPP sing 156 n n PA O1A GPP doub 157 n n PA O2A GPP sing 158 n n PA O3A GPP sing 159 n n O2A HOA2 GPP sing 160 n n O3A PB GPP sing 161 n n PB O1B GPP doub 162 n n PB O2B GPP sing 163 n n PB O3B GPP sing 164 n n O2B HOB2 GPP sing 165 n n O3B HOB3 GPP sing 166 n n # _atom_sites.entry_id 6YPF _atom_sites.fract_transf_matrix[1][1] 0.020289 _atom_sites.fract_transf_matrix[1][2] 0.011714 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023428 _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] 0.009589 _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 GPP A 1 201 201 GPP GPP . C 3 HOH A 1 301 112 HOH HOH . C 3 HOH A 2 302 106 HOH HOH . C 3 HOH A 3 303 26 HOH HOH . C 3 HOH A 4 304 47 HOH HOH . C 3 HOH A 5 305 89 HOH HOH . C 3 HOH A 6 306 40 HOH HOH . C 3 HOH A 7 307 33 HOH HOH . C 3 HOH A 8 308 12 HOH HOH . C 3 HOH A 9 309 78 HOH HOH . C 3 HOH A 10 310 103 HOH HOH . C 3 HOH A 11 311 22 HOH HOH . C 3 HOH A 12 312 37 HOH HOH . C 3 HOH A 13 313 17 HOH HOH . C 3 HOH A 14 314 16 HOH HOH . C 3 HOH A 15 315 58 HOH HOH . C 3 HOH A 16 316 32 HOH HOH . C 3 HOH A 17 317 77 HOH HOH . C 3 HOH A 18 318 5 HOH HOH . C 3 HOH A 19 319 35 HOH HOH . C 3 HOH A 20 320 2 HOH HOH . C 3 HOH A 21 321 15 HOH HOH . C 3 HOH A 22 322 1 HOH HOH . C 3 HOH A 23 323 7 HOH HOH . C 3 HOH A 24 324 71 HOH HOH . C 3 HOH A 25 325 51 HOH HOH . C 3 HOH A 26 326 50 HOH HOH . C 3 HOH A 27 327 99 HOH HOH . C 3 HOH A 28 328 27 HOH HOH . C 3 HOH A 29 329 90 HOH HOH . C 3 HOH A 30 330 52 HOH HOH . C 3 HOH A 31 331 4 HOH HOH . C 3 HOH A 32 332 87 HOH HOH . C 3 HOH A 33 333 18 HOH HOH . C 3 HOH A 34 334 14 HOH HOH . C 3 HOH A 35 335 42 HOH HOH . C 3 HOH A 36 336 10 HOH HOH . C 3 HOH A 37 337 61 HOH HOH . C 3 HOH A 38 338 25 HOH HOH . C 3 HOH A 39 339 13 HOH HOH . C 3 HOH A 40 340 48 HOH HOH . C 3 HOH A 41 341 11 HOH HOH . C 3 HOH A 42 342 109 HOH HOH . C 3 HOH A 43 343 6 HOH HOH . C 3 HOH A 44 344 41 HOH HOH . C 3 HOH A 45 345 44 HOH HOH . C 3 HOH A 46 346 3 HOH HOH . C 3 HOH A 47 347 9 HOH HOH . C 3 HOH A 48 348 57 HOH HOH . C 3 HOH A 49 349 21 HOH HOH . C 3 HOH A 50 350 20 HOH HOH . C 3 HOH A 51 351 66 HOH HOH . C 3 HOH A 52 352 23 HOH HOH . C 3 HOH A 53 353 19 HOH HOH . C 3 HOH A 54 354 46 HOH HOH . C 3 HOH A 55 355 65 HOH HOH . C 3 HOH A 56 356 70 HOH HOH . C 3 HOH A 57 357 107 HOH HOH . C 3 HOH A 58 358 98 HOH HOH . C 3 HOH A 59 359 24 HOH HOH . C 3 HOH A 60 360 55 HOH HOH . C 3 HOH A 61 361 62 HOH HOH . C 3 HOH A 62 362 28 HOH HOH . C 3 HOH A 63 363 113 HOH HOH . C 3 HOH A 64 364 92 HOH HOH . C 3 HOH A 65 365 43 HOH HOH . C 3 HOH A 66 366 111 HOH HOH . C 3 HOH A 67 367 93 HOH HOH . C 3 HOH A 68 368 60 HOH HOH . C 3 HOH A 69 369 29 HOH HOH . C 3 HOH A 70 370 38 HOH HOH . C 3 HOH A 71 371 101 HOH HOH . C 3 HOH A 72 372 45 HOH HOH . C 3 HOH A 73 373 83 HOH HOH . C 3 HOH A 74 374 74 HOH HOH . C 3 HOH A 75 375 49 HOH HOH . C 3 HOH A 76 376 114 HOH HOH . C 3 HOH A 77 377 36 HOH HOH . C 3 HOH A 78 378 108 HOH HOH . C 3 HOH A 79 379 69 HOH HOH . C 3 HOH A 80 380 86 HOH HOH . C 3 HOH A 81 381 39 HOH HOH . C 3 HOH A 82 382 54 HOH HOH . C 3 HOH A 83 383 110 HOH HOH . C 3 HOH A 84 384 75 HOH HOH . C 3 HOH A 85 385 8 HOH HOH . C 3 HOH A 86 386 56 HOH HOH . C 3 HOH A 87 387 72 HOH HOH . C 3 HOH A 88 388 104 HOH HOH . C 3 HOH A 89 389 95 HOH HOH . C 3 HOH A 90 390 115 HOH HOH . C 3 HOH A 91 391 73 HOH HOH . C 3 HOH A 92 392 76 HOH HOH . C 3 HOH A 93 393 82 HOH HOH . C 3 HOH A 94 394 97 HOH HOH . C 3 HOH A 95 395 63 HOH HOH . C 3 HOH A 96 396 31 HOH HOH . C 3 HOH A 97 397 53 HOH HOH . C 3 HOH A 98 398 79 HOH HOH . C 3 HOH A 99 399 30 HOH HOH . C 3 HOH A 100 400 59 HOH HOH . C 3 HOH A 101 401 80 HOH HOH . C 3 HOH A 102 402 34 HOH HOH . C 3 HOH A 103 403 81 HOH HOH . C 3 HOH A 104 404 88 HOH HOH . C 3 HOH A 105 405 68 HOH HOH . C 3 HOH A 106 406 64 HOH HOH . C 3 HOH A 107 407 100 HOH HOH . C 3 HOH A 108 408 67 HOH HOH . C 3 HOH A 109 409 85 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 GPP . . . B 2 -31.432 7.39 3.397 1 80.79 ? C1 GPP 201 A 1 HETATM 2 O O1 GPP . . . B 2 -31.873 7.279 4.725 1 86.4 ? O1 GPP 201 A 1 HETATM 3 C C2 GPP . . . B 2 -31.34 8.864 2.993 1 74.8 ? C2 GPP 201 A 1 HETATM 4 C C3 GPP . . . B 2 -31.219 9.226 1.725 1 68.76 ? C3 GPP 201 A 1 HETATM 5 C C4 GPP . . . B 2 -31.166 8.181 0.619 1 68.2 ? C4 GPP 201 A 1 HETATM 6 C C5 GPP . . . B 2 -31.134 10.712 1.394 1 63.58 ? C5 GPP 201 A 1 HETATM 7 C C6 GPP . . . B 2 -30.06 10.947 0.355 1 58.49 ? C6 GPP 201 A 1 HETATM 8 C C7 GPP . . . B 2 -29.343 12.269 0.587 1 53.87 ? C7 GPP 201 A 1 HETATM 9 C C8 GPP . . . B 2 -28.362 12.386 1.452 1 51.35 ? C8 GPP 201 A 1 HETATM 10 C C9 GPP . . . B 2 -27.919 11.219 2.32 1 51.37 ? C9 GPP 201 A 1 HETATM 11 C C10 GPP . . . B 2 -27.674 13.735 1.604 1 49.41 ? C10 GPP 201 A 1 HETATM 12 P PA GPP . . . B 2 -31.181 6.108 5.673 1 90.98 ? PA GPP 201 A 1 HETATM 13 O O1A GPP . . . B 2 -29.928 6.646 6.326 1 89.86 ? O1A GPP 201 A 1 HETATM 14 O O2A GPP . . . B 2 -32.159 5.687 6.749 1 94.63 ? O2A GPP 201 A 1 HETATM 15 O O3A GPP . . . B 2 -30.791 4.796 4.732 1 92.26 ? O3A GPP 201 A 1 HETATM 16 P PB GPP . . . B 2 -31.89 3.802 3.991 1 92.4 ? PB GPP 201 A 1 HETATM 17 O O1B GPP . . . B 2 -32.684 4.573 2.968 1 92.69 ? O1B GPP 201 A 1 HETATM 18 O O2B GPP . . . B 2 -32.836 3.228 5.019 1 91.94 ? O2B GPP 201 A 1 HETATM 19 O O3B GPP . . . B 2 -31.146 2.677 3.309 1 92.77 ? O3B GPP 201 A 1 HETATM 20 H H11 GPP . . . B 2 -30.453 6.931 3.305 1 96.99 ? H11 GPP 201 A 1 HETATM 21 H H12 GPP . . . B 2 -32.132 6.882 2.743 1 96.99 ? H12 GPP 201 A 1 HETATM 22 H H2 GPP . . . B 2 -31.375 9.627 3.761 1 89.79 ? H2 GPP 201 A 1 HETATM 23 H H41 GPP . . . B 2 -30.177 7.73 0.593 1 81.88 ? H41 GPP 201 A 1 HETATM 24 H H42 GPP . . . B 2 -31.91 7.412 0.811 1 81.88 ? H42 GPP 201 A 1 HETATM 25 H H43 GPP . . . B 2 -31.373 8.654 -0.338 1 81.88 ? H43 GPP 201 A 1 HETATM 26 H H51 GPP . . . B 2 -30.891 11.268 2.293 1 76.33 ? H51 GPP 201 A 1 HETATM 27 H H52 GPP . . . B 2 -32.089 11.05 1.007 1 76.33 ? H52 GPP 201 A 1 HETATM 28 H H61 GPP . . . B 2 -29.338 10.14 0.405 1 70.22 ? H61 GPP 201 A 1 HETATM 29 H H62 GPP . . . B 2 -30.518 10.962 -0.629 1 70.22 ? H62 GPP 201 A 1 HETATM 30 H H7 GPP . . . B 2 -29.652 13.14 0.022 1 64.69 ? H7 GPP 201 A 1 HETATM 31 H H91 GPP . . . B 2 -27.109 11.539 2.971 1 61.69 ? H91 GPP 201 A 1 HETATM 32 H H92 GPP . . . B 2 -27.575 10.406 1.685 1 61.69 ? H92 GPP 201 A 1 HETATM 33 H H93 GPP . . . B 2 -28.756 10.879 2.923 1 61.69 ? H93 GPP 201 A 1 HETATM 34 H H101 GPP . . . B 2 -28.405 14.483 1.895 1 59.33 ? H101 GPP 201 A 1 HETATM 35 H H102 GPP . . . B 2 -27.221 14.019 0.659 1 59.33 ? H102 GPP 201 A 1 HETATM 36 H H103 GPP . . . B 2 -26.904 13.664 2.368 1 59.33 ? H103 GPP 201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #