data_4YZL # _model_server_result.job_id ehcmV75j0dlOy4Q5K2SftA _model_server_result.datetime_utc '2025-03-02 22:27:34' _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 4yzl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4YZL # _exptl.entry_id 4YZL _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 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 90 _cell.entry_id 4YZL _cell.length_a 42.38 _cell.length_b 74.1 _cell.length_c 112.16 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YZL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 83 n n O4 HO4 DST sing 84 n n P1 O6 DST sing 85 n n P1 O5 DST doub 86 n n P1 O2 DST sing 87 n n O6 HO6 DST sing 88 n n O2 P3 DST sing 89 n n P3 O8 DST sing 90 n n P3 O7 DST doub 91 n n P3 S9 DST sing 92 n n O8 HO8 DST sing 93 n n S9 C10 DST sing 94 n n C10 C11 DST sing 95 n n C10 H101 DST sing 96 n n C10 H102 DST sing 97 n n C11 C12 DST doub 98 n n C11 H111 DST sing 99 n n C12 C13 DST sing 100 n n C12 C14 DST sing 101 n n C13 H131 DST sing 102 n n C13 H132 DST sing 103 n n C13 H133 DST sing 104 n n C14 H141 DST sing 105 n n C14 H142 DST sing 106 n n C14 H143 DST sing 107 n n # _atom_sites.entry_id 4YZL _atom_sites.fract_transf_matrix[1][1] 0.023596 _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] 0.013495 _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] 0.008916 _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 ILV A 1 401 1 ILV ILV . C 3 DST A 1 402 1 DST DST . D 4 HOH A 1 501 98 HOH HOH . D 4 HOH A 2 502 119 HOH HOH . D 4 HOH A 3 503 12 HOH HOH . D 4 HOH A 4 504 141 HOH HOH . D 4 HOH A 5 505 93 HOH HOH . D 4 HOH A 6 506 51 HOH HOH . D 4 HOH A 7 507 40 HOH HOH . D 4 HOH A 8 508 118 HOH HOH . D 4 HOH A 9 509 44 HOH HOH . D 4 HOH A 10 510 61 HOH HOH . D 4 HOH A 11 511 45 HOH HOH . D 4 HOH A 12 512 53 HOH HOH . D 4 HOH A 13 513 39 HOH HOH . D 4 HOH A 14 514 101 HOH HOH . D 4 HOH A 15 515 163 HOH HOH . D 4 HOH A 16 516 4 HOH HOH . D 4 HOH A 17 517 19 HOH HOH . D 4 HOH A 18 518 66 HOH HOH . D 4 HOH A 19 519 17 HOH HOH . D 4 HOH A 20 520 31 HOH HOH . D 4 HOH A 21 521 7 HOH HOH . D 4 HOH A 22 522 8 HOH HOH . D 4 HOH A 23 523 145 HOH HOH . D 4 HOH A 24 524 171 HOH HOH . D 4 HOH A 25 525 128 HOH HOH . D 4 HOH A 26 526 178 HOH HOH . D 4 HOH A 27 527 75 HOH HOH . D 4 HOH A 28 528 154 HOH HOH . D 4 HOH A 29 529 22 HOH HOH . D 4 HOH A 30 530 85 HOH HOH . D 4 HOH A 31 531 26 HOH HOH . D 4 HOH A 32 532 59 HOH HOH . D 4 HOH A 33 533 65 HOH HOH . D 4 HOH A 34 534 68 HOH HOH . D 4 HOH A 35 535 108 HOH HOH . D 4 HOH A 36 536 74 HOH HOH . D 4 HOH A 37 537 62 HOH HOH . D 4 HOH A 38 538 37 HOH HOH . D 4 HOH A 39 539 102 HOH HOH . D 4 HOH A 40 540 153 HOH HOH . D 4 HOH A 41 541 21 HOH HOH . D 4 HOH A 42 542 52 HOH HOH . D 4 HOH A 43 543 46 HOH HOH . D 4 HOH A 44 544 20 HOH HOH . D 4 HOH A 45 545 135 HOH HOH . D 4 HOH A 46 546 1 HOH HOH . D 4 HOH A 47 547 2 HOH HOH . D 4 HOH A 48 548 67 HOH HOH . D 4 HOH A 49 549 24 HOH HOH . D 4 HOH A 50 550 5 HOH HOH . D 4 HOH A 51 551 161 HOH HOH . D 4 HOH A 52 552 47 HOH HOH . D 4 HOH A 53 553 109 HOH HOH . D 4 HOH A 54 554 54 HOH HOH . D 4 HOH A 55 555 121 HOH HOH . D 4 HOH A 56 556 110 HOH HOH . D 4 HOH A 57 557 3 HOH HOH . D 4 HOH A 58 558 90 HOH HOH . D 4 HOH A 59 559 188 HOH HOH . D 4 HOH A 60 560 58 HOH HOH . D 4 HOH A 61 561 43 HOH HOH . D 4 HOH A 62 562 81 HOH HOH . D 4 HOH A 63 563 55 HOH HOH . D 4 HOH A 64 564 13 HOH HOH . D 4 HOH A 65 565 123 HOH HOH . D 4 HOH A 66 566 140 HOH HOH . D 4 HOH A 67 567 166 HOH HOH . D 4 HOH A 68 568 41 HOH HOH . D 4 HOH A 69 569 165 HOH HOH . D 4 HOH A 70 570 106 HOH HOH . D 4 HOH A 71 571 92 HOH HOH . D 4 HOH A 72 572 137 HOH HOH . D 4 HOH A 73 573 32 HOH HOH . D 4 HOH A 74 574 91 HOH HOH . D 4 HOH A 75 575 60 HOH HOH . D 4 HOH A 76 576 86 HOH HOH . D 4 HOH A 77 577 6 HOH HOH . D 4 HOH A 78 578 72 HOH HOH . D 4 HOH A 79 579 76 HOH HOH . D 4 HOH A 80 580 38 HOH HOH . D 4 HOH A 81 581 30 HOH HOH . D 4 HOH A 82 582 84 HOH HOH . D 4 HOH A 83 583 79 HOH HOH . D 4 HOH A 84 584 49 HOH HOH . D 4 HOH A 85 585 64 HOH HOH . D 4 HOH A 86 586 126 HOH HOH . D 4 HOH A 87 587 18 HOH HOH . D 4 HOH A 88 588 29 HOH HOH . D 4 HOH A 89 589 122 HOH HOH . D 4 HOH A 90 590 125 HOH HOH . D 4 HOH A 91 591 180 HOH HOH . D 4 HOH A 92 592 116 HOH HOH . D 4 HOH A 93 593 16 HOH HOH . D 4 HOH A 94 594 96 HOH HOH . D 4 HOH A 95 595 150 HOH HOH . D 4 HOH A 96 596 69 HOH HOH . D 4 HOH A 97 597 95 HOH HOH . D 4 HOH A 98 598 11 HOH HOH . D 4 HOH A 99 599 173 HOH HOH . D 4 HOH A 100 600 97 HOH HOH . D 4 HOH A 101 601 100 HOH HOH . D 4 HOH A 102 602 149 HOH HOH . D 4 HOH A 103 603 88 HOH HOH . D 4 HOH A 104 604 48 HOH HOH . D 4 HOH A 105 605 78 HOH HOH . D 4 HOH A 106 606 184 HOH HOH . D 4 HOH A 107 607 35 HOH HOH . D 4 HOH A 108 608 143 HOH HOH . D 4 HOH A 109 609 113 HOH HOH . D 4 HOH A 110 610 27 HOH HOH . D 4 HOH A 111 611 9 HOH HOH . D 4 HOH A 112 612 177 HOH HOH . D 4 HOH A 113 613 117 HOH HOH . D 4 HOH A 114 614 133 HOH HOH . D 4 HOH A 115 615 115 HOH HOH . D 4 HOH A 116 616 107 HOH HOH . D 4 HOH A 117 617 71 HOH HOH . D 4 HOH A 118 618 160 HOH HOH . D 4 HOH A 119 619 94 HOH HOH . D 4 HOH A 120 620 28 HOH HOH . D 4 HOH A 121 621 34 HOH HOH . D 4 HOH A 122 622 130 HOH HOH . D 4 HOH A 123 623 162 HOH HOH . D 4 HOH A 124 624 146 HOH HOH . D 4 HOH A 125 625 33 HOH HOH . D 4 HOH A 126 626 156 HOH HOH . D 4 HOH A 127 627 175 HOH HOH . D 4 HOH A 128 628 132 HOH HOH . D 4 HOH A 129 629 168 HOH HOH . D 4 HOH A 130 630 82 HOH HOH . D 4 HOH A 131 631 103 HOH HOH . D 4 HOH A 132 632 174 HOH HOH . D 4 HOH A 133 633 151 HOH HOH . D 4 HOH A 134 634 148 HOH HOH . D 4 HOH A 135 635 158 HOH HOH . D 4 HOH A 136 636 112 HOH HOH . D 4 HOH A 137 637 138 HOH HOH . D 4 HOH A 138 638 14 HOH HOH . D 4 HOH A 139 639 187 HOH HOH . D 4 HOH A 140 640 144 HOH HOH . D 4 HOH A 141 641 83 HOH HOH . D 4 HOH A 142 642 170 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 . . . C 3 21.842 83.95 17.95 0.7 33.65 ? O4 DST 402 A 1 HETATM 2 P P1 DST . . . C 3 21.448 82.708 17.009 0.7 32.73 ? P1 DST 402 A 1 HETATM 3 O O6 DST . . . C 3 22.379 81.461 17.501 0.7 36.11 ? O6 DST 402 A 1 HETATM 4 O O5 DST . . . C 3 21.799 83.051 15.629 0.7 34.46 ? O5 DST 402 A 1 HETATM 5 O O2 DST . . . C 3 19.861 82.293 17.29 0.7 33.73 ? O2 DST 402 A 1 HETATM 6 P P3 DST . . . C 3 19.101 81.31 16.19 0.7 39.6 ? P3 DST 402 A 1 HETATM 7 O O8 DST . . . C 3 19.566 79.889 16.281 0.7 30.87 ? O8 DST 402 A 1 HETATM 8 O O7 DST . . . C 3 19.414 81.983 14.747 0.7 25.95 ? O7 DST 402 A 1 HETATM 9 S S9 DST . . . C 3 17.364 81.35 16.347 0.7 41.5 ? S9 DST 402 A 1 HETATM 10 C C10 DST . . . C 3 16.946 79.648 15.727 0.7 24.33 ? C10 DST 402 A 1 HETATM 11 C C11 DST . . . C 3 15.576 79.244 16.345 0.7 25.44 ? C11 DST 402 A 1 HETATM 12 C C12 DST . . . C 3 14.936 77.917 15.927 0.7 25.23 ? C12 DST 402 A 1 HETATM 13 C C13 DST . . . C 3 13.607 77.503 16.548 0.7 24.13 ? C13 DST 402 A 1 HETATM 14 C C14 DST . . . C 3 15.6 77.004 14.899 0.7 23.37 ? C14 DST 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #