data_5Y84 # _model_server_result.job_id B905roEckEfmQPnSxejLLA _model_server_result.datetime_utc '2024-11-19 05:35:39' _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 5y84 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5Y84 # _exptl.entry_id 5Y84 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 262.158 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIMETHYLALLYL S-THIOLODIPHOSPHATE' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 105.42 _cell.angle_beta 106.24 _cell.angle_gamma 98.68 _cell.entry_id 5Y84 _cell.length_a 46.311 _cell.length_b 54.81 _cell.length_c 77.087 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y84 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,G 1 1 B,E,F,H 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C5 H12 O6 P2 S' _chem_comp.formula_weight 262.158 _chem_comp.id DST _chem_comp.mon_nstd_flag . _chem_comp.name 'DIMETHYLALLYL S-THIOLODIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'DMASPP;DMAPP;DMADP;Dimethylallyl pyrophosphate;dimethylallyl diphosphate;isoprenyl 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 O4 P1 DST sing 133 n n O4 HO4 DST sing 134 n n P1 O6 DST sing 135 n n P1 O5 DST doub 136 n n P1 O2 DST sing 137 n n O6 HO6 DST sing 138 n n O2 P3 DST sing 139 n n P3 O8 DST sing 140 n n P3 O7 DST doub 141 n n P3 S9 DST sing 142 n n O8 HO8 DST sing 143 n n S9 C10 DST sing 144 n n C10 C11 DST sing 145 n n C10 H101 DST sing 146 n n C10 H102 DST sing 147 n n C11 C12 DST doub 148 n n C11 H111 DST sing 149 n n C12 C13 DST sing 150 n n C12 C14 DST sing 151 n n C13 H131 DST sing 152 n n C13 H132 DST sing 153 n n C13 H133 DST sing 154 n n C14 H141 DST sing 155 n n C14 H142 DST sing 156 n n C14 H143 DST sing 157 n n # _atom_sites.entry_id 5Y84 _atom_sites.fract_transf_matrix[1][1] 0.021593 _atom_sites.fract_transf_matrix[1][2] 0.003298 _atom_sites.fract_transf_matrix[1][3] 0.007781 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018456 _atom_sites.fract_transf_matrix[2][3] 0.006334 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.014285 _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 8P6 A 1 401 1 8P6 HUS . D 3 DST A 1 402 2 DST DST . E 2 8P6 B 1 401 3 8P6 HUS . F 3 DST B 1 402 4 DST DST . G 4 HOH A 1 501 193 HOH HOH . G 4 HOH A 2 502 220 HOH HOH . G 4 HOH A 3 503 39 HOH HOH . G 4 HOH A 4 504 60 HOH HOH . G 4 HOH A 5 505 125 HOH HOH . G 4 HOH A 6 506 79 HOH HOH . G 4 HOH A 7 507 12 HOH HOH . G 4 HOH A 8 508 260 HOH HOH . G 4 HOH A 9 509 154 HOH HOH . G 4 HOH A 10 510 124 HOH HOH . G 4 HOH A 11 511 158 HOH HOH . G 4 HOH A 12 512 140 HOH HOH . G 4 HOH A 13 513 344 HOH HOH . G 4 HOH A 14 514 82 HOH HOH . G 4 HOH A 15 515 133 HOH HOH . G 4 HOH A 16 516 24 HOH HOH . G 4 HOH A 17 517 100 HOH HOH . G 4 HOH A 18 518 136 HOH HOH . G 4 HOH A 19 519 326 HOH HOH . G 4 HOH A 20 520 6 HOH HOH . G 4 HOH A 21 521 76 HOH HOH . G 4 HOH A 22 522 141 HOH HOH . G 4 HOH A 23 523 173 HOH HOH . G 4 HOH A 24 524 85 HOH HOH . G 4 HOH A 25 525 77 HOH HOH . G 4 HOH A 26 526 226 HOH HOH . G 4 HOH A 27 527 73 HOH HOH . G 4 HOH A 28 528 149 HOH HOH . G 4 HOH A 29 529 132 HOH HOH . G 4 HOH A 30 530 8 HOH HOH . G 4 HOH A 31 531 59 HOH HOH . G 4 HOH A 32 532 78 HOH HOH . G 4 HOH A 33 533 36 HOH HOH . G 4 HOH A 34 534 10 HOH HOH . G 4 HOH A 35 535 178 HOH HOH . G 4 HOH A 36 536 49 HOH HOH . G 4 HOH A 37 537 194 HOH HOH . G 4 HOH A 38 538 64 HOH HOH . G 4 HOH A 39 539 5 HOH HOH . G 4 HOH A 40 540 308 HOH HOH . G 4 HOH A 41 541 47 HOH HOH . G 4 HOH A 42 542 185 HOH HOH . G 4 HOH A 43 543 330 HOH HOH . G 4 HOH A 44 544 22 HOH HOH . G 4 HOH A 45 545 179 HOH HOH . G 4 HOH A 46 546 201 HOH HOH . G 4 HOH A 47 547 112 HOH HOH . G 4 HOH A 48 548 45 HOH HOH . G 4 HOH A 49 549 48 HOH HOH . G 4 HOH A 50 550 176 HOH HOH . G 4 HOH A 51 551 17 HOH HOH . G 4 HOH A 52 552 107 HOH HOH . G 4 HOH A 53 553 117 HOH HOH . G 4 HOH A 54 554 114 HOH HOH . G 4 HOH A 55 555 170 HOH HOH . G 4 HOH A 56 556 28 HOH HOH . G 4 HOH A 57 557 14 HOH HOH . G 4 HOH A 58 558 81 HOH HOH . G 4 HOH A 59 559 51 HOH HOH . G 4 HOH A 60 560 142 HOH HOH . G 4 HOH A 61 561 186 HOH HOH . G 4 HOH A 62 562 65 HOH HOH . G 4 HOH A 63 563 83 HOH HOH . G 4 HOH A 64 564 111 HOH HOH . G 4 HOH A 65 565 54 HOH HOH . G 4 HOH A 66 566 214 HOH HOH . G 4 HOH A 67 567 152 HOH HOH . G 4 HOH A 68 568 188 HOH HOH . G 4 HOH A 69 569 129 HOH HOH . G 4 HOH A 70 570 227 HOH HOH . G 4 HOH A 71 571 161 HOH HOH . G 4 HOH A 72 572 259 HOH HOH . G 4 HOH A 73 573 225 HOH HOH . G 4 HOH A 74 574 270 HOH HOH . G 4 HOH A 75 575 192 HOH HOH . G 4 HOH A 76 576 223 HOH HOH . G 4 HOH A 77 577 50 HOH HOH . G 4 HOH A 78 578 241 HOH HOH . G 4 HOH A 79 579 42 HOH HOH . G 4 HOH A 80 580 221 HOH HOH . G 4 HOH A 81 581 89 HOH HOH . G 4 HOH A 82 582 127 HOH HOH . G 4 HOH A 83 583 323 HOH HOH . G 4 HOH A 84 584 187 HOH HOH . G 4 HOH A 85 585 31 HOH HOH . G 4 HOH A 86 586 38 HOH HOH . G 4 HOH A 87 587 57 HOH HOH . G 4 HOH A 88 588 27 HOH HOH . G 4 HOH A 89 589 84 HOH HOH . G 4 HOH A 90 590 294 HOH HOH . G 4 HOH A 91 591 91 HOH HOH . G 4 HOH A 92 592 99 HOH HOH . G 4 HOH A 93 593 310 HOH HOH . G 4 HOH A 94 594 198 HOH HOH . G 4 HOH A 95 595 217 HOH HOH . G 4 HOH A 96 596 210 HOH HOH . G 4 HOH A 97 597 63 HOH HOH . G 4 HOH A 98 598 228 HOH HOH . G 4 HOH A 99 599 343 HOH HOH . G 4 HOH A 100 600 138 HOH HOH . G 4 HOH A 101 601 243 HOH HOH . G 4 HOH A 102 602 86 HOH HOH . G 4 HOH A 103 603 340 HOH HOH . G 4 HOH A 104 604 281 HOH HOH . G 4 HOH A 105 605 233 HOH HOH . G 4 HOH A 106 606 254 HOH HOH . G 4 HOH A 107 607 312 HOH HOH . G 4 HOH A 108 608 131 HOH HOH . G 4 HOH A 109 609 52 HOH HOH . G 4 HOH A 110 610 235 HOH HOH . G 4 HOH A 111 611 317 HOH HOH . G 4 HOH A 112 612 118 HOH HOH . G 4 HOH A 113 613 319 HOH HOH . G 4 HOH A 114 614 20 HOH HOH . G 4 HOH A 115 615 283 HOH HOH . G 4 HOH A 116 616 272 HOH HOH . G 4 HOH A 117 617 80 HOH HOH . G 4 HOH A 118 618 273 HOH HOH . G 4 HOH A 119 619 209 HOH HOH . G 4 HOH A 120 620 174 HOH HOH . G 4 HOH A 121 621 94 HOH HOH . G 4 HOH A 122 622 262 HOH HOH . G 4 HOH A 123 623 121 HOH HOH . G 4 HOH A 124 624 293 HOH HOH . G 4 HOH A 125 625 145 HOH HOH . G 4 HOH A 126 626 134 HOH HOH . G 4 HOH A 127 627 122 HOH HOH . G 4 HOH A 128 628 204 HOH HOH . G 4 HOH A 129 629 279 HOH HOH . G 4 HOH A 130 630 182 HOH HOH . G 4 HOH A 131 631 284 HOH HOH . G 4 HOH A 132 632 287 HOH HOH . G 4 HOH A 133 633 253 HOH HOH . G 4 HOH A 134 634 148 HOH HOH . G 4 HOH A 135 635 237 HOH HOH . G 4 HOH A 136 636 313 HOH HOH . G 4 HOH A 137 637 311 HOH HOH . G 4 HOH A 138 638 206 HOH HOH . G 4 HOH A 139 639 335 HOH HOH . G 4 HOH A 140 640 216 HOH HOH . G 4 HOH A 141 641 239 HOH HOH . G 4 HOH A 142 642 302 HOH HOH . G 4 HOH A 143 643 324 HOH HOH . G 4 HOH A 144 644 342 HOH HOH . G 4 HOH A 145 645 280 HOH HOH . G 4 HOH A 146 646 328 HOH HOH . G 4 HOH A 147 647 299 HOH HOH . H 4 HOH B 1 501 41 HOH HOH . H 4 HOH B 2 502 200 HOH HOH . H 4 HOH B 3 503 66 HOH HOH . H 4 HOH B 4 504 29 HOH HOH . H 4 HOH B 5 505 90 HOH HOH . H 4 HOH B 6 506 62 HOH HOH . H 4 HOH B 7 507 305 HOH HOH . H 4 HOH B 8 508 261 HOH HOH . H 4 HOH B 9 509 67 HOH HOH . H 4 HOH B 10 510 11 HOH HOH . H 4 HOH B 11 511 349 HOH HOH . H 4 HOH B 12 512 267 HOH HOH . H 4 HOH B 13 513 203 HOH HOH . H 4 HOH B 14 514 2 HOH HOH . H 4 HOH B 15 515 180 HOH HOH . H 4 HOH B 16 516 97 HOH HOH . H 4 HOH B 17 517 175 HOH HOH . H 4 HOH B 18 518 40 HOH HOH . H 4 HOH B 19 519 3 HOH HOH . H 4 HOH B 20 520 128 HOH HOH . H 4 HOH B 21 521 120 HOH HOH . H 4 HOH B 22 522 113 HOH HOH . H 4 HOH B 23 523 105 HOH HOH . H 4 HOH B 24 524 98 HOH HOH . H 4 HOH B 25 525 147 HOH HOH . H 4 HOH B 26 526 265 HOH HOH . H 4 HOH B 27 527 56 HOH HOH . H 4 HOH B 28 528 1 HOH HOH . H 4 HOH B 29 529 232 HOH HOH . H 4 HOH B 30 530 13 HOH HOH . H 4 HOH B 31 531 181 HOH HOH . H 4 HOH B 32 532 7 HOH HOH . H 4 HOH B 33 533 171 HOH HOH . H 4 HOH B 34 534 205 HOH HOH . H 4 HOH B 35 535 44 HOH HOH . H 4 HOH B 36 536 33 HOH HOH . H 4 HOH B 37 537 15 HOH HOH . H 4 HOH B 38 538 35 HOH HOH . H 4 HOH B 39 539 4 HOH HOH . H 4 HOH B 40 540 166 HOH HOH . H 4 HOH B 41 541 92 HOH HOH . H 4 HOH B 42 542 19 HOH HOH . H 4 HOH B 43 543 202 HOH HOH . H 4 HOH B 44 544 9 HOH HOH . H 4 HOH B 45 545 292 HOH HOH . H 4 HOH B 46 546 137 HOH HOH . H 4 HOH B 47 547 18 HOH HOH . H 4 HOH B 48 548 75 HOH HOH . H 4 HOH B 49 549 282 HOH HOH . H 4 HOH B 50 550 151 HOH HOH . H 4 HOH B 51 551 274 HOH HOH . H 4 HOH B 52 552 163 HOH HOH . H 4 HOH B 53 553 88 HOH HOH . H 4 HOH B 54 554 108 HOH HOH . H 4 HOH B 55 555 25 HOH HOH . H 4 HOH B 56 556 304 HOH HOH . H 4 HOH B 57 557 37 HOH HOH . H 4 HOH B 58 558 197 HOH HOH . H 4 HOH B 59 559 61 HOH HOH . H 4 HOH B 60 560 172 HOH HOH . H 4 HOH B 61 561 58 HOH HOH . H 4 HOH B 62 562 30 HOH HOH . H 4 HOH B 63 563 70 HOH HOH . H 4 HOH B 64 564 277 HOH HOH . H 4 HOH B 65 565 16 HOH HOH . H 4 HOH B 66 566 162 HOH HOH . H 4 HOH B 67 567 21 HOH HOH . H 4 HOH B 68 568 119 HOH HOH . H 4 HOH B 69 569 26 HOH HOH . H 4 HOH B 70 570 177 HOH HOH . H 4 HOH B 71 571 55 HOH HOH . H 4 HOH B 72 572 116 HOH HOH . H 4 HOH B 73 573 126 HOH HOH . H 4 HOH B 74 574 102 HOH HOH . H 4 HOH B 75 575 68 HOH HOH . H 4 HOH B 76 576 244 HOH HOH . H 4 HOH B 77 577 32 HOH HOH . H 4 HOH B 78 578 150 HOH HOH . H 4 HOH B 79 579 212 HOH HOH . H 4 HOH B 80 580 160 HOH HOH . H 4 HOH B 81 581 252 HOH HOH . H 4 HOH B 82 582 123 HOH HOH . H 4 HOH B 83 583 271 HOH HOH . H 4 HOH B 84 584 135 HOH HOH . H 4 HOH B 85 585 157 HOH HOH . H 4 HOH B 86 586 34 HOH HOH . H 4 HOH B 87 587 156 HOH HOH . H 4 HOH B 88 588 268 HOH HOH . H 4 HOH B 89 589 144 HOH HOH . H 4 HOH B 90 590 183 HOH HOH . H 4 HOH B 91 591 109 HOH HOH . H 4 HOH B 92 592 339 HOH HOH . H 4 HOH B 93 593 95 HOH HOH . H 4 HOH B 94 594 93 HOH HOH . H 4 HOH B 95 595 74 HOH HOH . H 4 HOH B 96 596 164 HOH HOH . H 4 HOH B 97 597 72 HOH HOH . H 4 HOH B 98 598 249 HOH HOH . H 4 HOH B 99 599 236 HOH HOH . H 4 HOH B 100 600 248 HOH HOH . H 4 HOH B 101 601 229 HOH HOH . H 4 HOH B 102 602 53 HOH HOH . H 4 HOH B 103 603 275 HOH HOH . H 4 HOH B 104 604 190 HOH HOH . H 4 HOH B 105 605 320 HOH HOH . H 4 HOH B 106 606 208 HOH HOH . H 4 HOH B 107 607 230 HOH HOH . H 4 HOH B 108 608 256 HOH HOH . H 4 HOH B 109 609 103 HOH HOH . H 4 HOH B 110 610 327 HOH HOH . H 4 HOH B 111 611 250 HOH HOH . H 4 HOH B 112 612 101 HOH HOH . H 4 HOH B 113 613 301 HOH HOH . H 4 HOH B 114 614 338 HOH HOH . H 4 HOH B 115 615 153 HOH HOH . H 4 HOH B 116 616 257 HOH HOH . H 4 HOH B 117 617 222 HOH HOH . H 4 HOH B 118 618 322 HOH HOH . H 4 HOH B 119 619 211 HOH HOH . H 4 HOH B 120 620 263 HOH HOH . H 4 HOH B 121 621 43 HOH HOH . H 4 HOH B 122 622 71 HOH HOH . H 4 HOH B 123 623 285 HOH HOH . H 4 HOH B 124 624 46 HOH HOH . H 4 HOH B 125 625 110 HOH HOH . H 4 HOH B 126 626 306 HOH HOH . H 4 HOH B 127 627 251 HOH HOH . H 4 HOH B 128 628 139 HOH HOH . H 4 HOH B 129 629 289 HOH HOH . H 4 HOH B 130 630 247 HOH HOH . H 4 HOH B 131 631 130 HOH HOH . H 4 HOH B 132 632 240 HOH HOH . H 4 HOH B 133 633 255 HOH HOH . H 4 HOH B 134 634 104 HOH HOH . H 4 HOH B 135 635 269 HOH HOH . H 4 HOH B 136 636 264 HOH HOH . H 4 HOH B 137 637 191 HOH HOH . H 4 HOH B 138 638 106 HOH HOH . H 4 HOH B 139 639 168 HOH HOH . H 4 HOH B 140 640 266 HOH HOH . H 4 HOH B 141 641 315 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 O4 DST . . . D 3 9.89 20.379 41.374 1 37.25 ? O4 DST 402 A 1 HETATM 2 P P1 DST . . . D 3 9.768 20.11 39.892 1 38.34 ? P1 DST 402 A 1 HETATM 3 O O6 DST . . . D 3 10.803 19.077 39.507 1 32.13 -1 O6 DST 402 A 1 HETATM 4 O O5 DST . . . D 3 9.939 21.39 39.096 1 30.69 -1 O5 DST 402 A 1 HETATM 5 O O2 DST . . . D 3 8.243 19.558 39.649 1 38 ? O2 DST 402 A 1 HETATM 6 P P3 DST . . . D 3 7.718 18.368 38.659 1 34.35 ? P3 DST 402 A 1 HETATM 7 O O8 DST . . . D 3 8.375 17.039 38.88 1 36.4 ? O8 DST 402 A 1 HETATM 8 O O7 DST . . . D 3 7.854 18.817 37.229 1 42.87 -1 O7 DST 402 A 1 HETATM 9 S S9 DST . . . D 3 5.659 18.162 39.106 1 50.52 ? S9 DST 402 A 1 HETATM 10 C C10 DST . . . D 3 5.119 16.785 38.052 1 41.87 ? C10 DST 402 A 1 HETATM 11 C C11 DST . . . D 3 3.656 16.966 37.678 1 37.53 ? C11 DST 402 A 1 HETATM 12 C C12 DST . . . D 3 3.438 16.892 36.167 1 43.47 ? C12 DST 402 A 1 HETATM 13 C C13 DST . . . D 3 4.762 16.944 35.405 1 41.76 ? C13 DST 402 A 1 HETATM 14 C C14 DST . . . D 3 2.58 18.084 35.768 1 31.67 ? C14 DST 402 A 1 # _model_server_stats.io_time_ms 121 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #