data_7W8Y # _model_server_result.job_id xt_YIMrIEjsru1W5KRf2vQ _model_server_result.datetime_utc '2025-06-21 11:47:11' _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 7w8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7W8Y # _exptl.entry_id 7W8Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 262.158 _entity.id 2 _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 97.325 _cell.angle_gamma 90 _cell.entry_id 7W8Y _cell.length_a 49.521 _cell.length_b 44.714 _cell.length_c 78.384 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W8Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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,D,E,F,G _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 207 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 223 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id O7 _struct_conn.ptnr2_label_comp_id DST _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id DST _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.301 _struct_conn.pdbx_value_order ? # _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 7W8Y _atom_sites.fract_transf_matrix[1][1] 0.020193 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002596 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022364 _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] 0.012863 _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 DST A 1 401 401 DST 6C7 . C 3 SO4 A 1 402 601 SO4 SO4 . D 4 TRS A 1 403 701 TRS TRS . E 5 DTT A 1 404 801 DTT DTT . F 6 E9M A 1 405 901 E9M E9M . G 7 HOH A 1 501 143 HOH HOH . G 7 HOH A 2 502 206 HOH HOH . G 7 HOH A 3 503 225 HOH HOH . G 7 HOH A 4 504 98 HOH HOH . G 7 HOH A 5 505 155 HOH HOH . G 7 HOH A 6 506 35 HOH HOH . G 7 HOH A 7 507 123 HOH HOH . G 7 HOH A 8 508 95 HOH HOH . G 7 HOH A 9 509 149 HOH HOH . G 7 HOH A 10 510 36 HOH HOH . G 7 HOH A 11 511 215 HOH HOH . G 7 HOH A 12 512 90 HOH HOH . G 7 HOH A 13 513 138 HOH HOH . G 7 HOH A 14 514 227 HOH HOH . G 7 HOH A 15 515 161 HOH HOH . G 7 HOH A 16 516 135 HOH HOH . G 7 HOH A 17 517 234 HOH HOH . G 7 HOH A 18 518 194 HOH HOH . G 7 HOH A 19 519 164 HOH HOH . G 7 HOH A 20 520 198 HOH HOH . G 7 HOH A 21 521 10 HOH HOH . G 7 HOH A 22 522 163 HOH HOH . G 7 HOH A 23 523 101 HOH HOH . G 7 HOH A 24 524 114 HOH HOH . G 7 HOH A 25 525 200 HOH HOH . G 7 HOH A 26 526 113 HOH HOH . G 7 HOH A 27 527 6 HOH HOH . G 7 HOH A 28 528 11 HOH HOH . G 7 HOH A 29 529 181 HOH HOH . G 7 HOH A 30 530 75 HOH HOH . G 7 HOH A 31 531 102 HOH HOH . G 7 HOH A 32 532 39 HOH HOH . G 7 HOH A 33 533 58 HOH HOH . G 7 HOH A 34 534 249 HOH HOH . G 7 HOH A 35 535 28 HOH HOH . G 7 HOH A 36 536 96 HOH HOH . G 7 HOH A 37 537 204 HOH HOH . G 7 HOH A 38 538 76 HOH HOH . G 7 HOH A 39 539 223 HOH HOH . G 7 HOH A 40 540 12 HOH HOH . G 7 HOH A 41 541 158 HOH HOH . G 7 HOH A 42 542 51 HOH HOH . G 7 HOH A 43 543 27 HOH HOH . G 7 HOH A 44 544 110 HOH HOH . G 7 HOH A 45 545 63 HOH HOH . G 7 HOH A 46 546 64 HOH HOH . G 7 HOH A 47 547 9 HOH HOH . G 7 HOH A 48 548 65 HOH HOH . G 7 HOH A 49 549 77 HOH HOH . G 7 HOH A 50 550 213 HOH HOH . G 7 HOH A 51 551 62 HOH HOH . G 7 HOH A 52 552 61 HOH HOH . G 7 HOH A 53 553 25 HOH HOH . G 7 HOH A 54 554 8 HOH HOH . G 7 HOH A 55 555 41 HOH HOH . G 7 HOH A 56 556 162 HOH HOH . G 7 HOH A 57 557 112 HOH HOH . G 7 HOH A 58 558 145 HOH HOH . G 7 HOH A 59 559 81 HOH HOH . G 7 HOH A 60 560 5 HOH HOH . G 7 HOH A 61 561 147 HOH HOH . G 7 HOH A 62 562 156 HOH HOH . G 7 HOH A 63 563 14 HOH HOH . G 7 HOH A 64 564 142 HOH HOH . G 7 HOH A 65 565 37 HOH HOH . G 7 HOH A 66 566 78 HOH HOH . G 7 HOH A 67 567 66 HOH HOH . G 7 HOH A 68 568 191 HOH HOH . G 7 HOH A 69 569 29 HOH HOH . G 7 HOH A 70 570 2 HOH HOH . G 7 HOH A 71 571 17 HOH HOH . G 7 HOH A 72 572 19 HOH HOH . G 7 HOH A 73 573 21 HOH HOH . G 7 HOH A 74 574 72 HOH HOH . G 7 HOH A 75 575 117 HOH HOH . G 7 HOH A 76 576 222 HOH HOH . G 7 HOH A 77 577 54 HOH HOH . G 7 HOH A 78 578 154 HOH HOH . G 7 HOH A 79 579 53 HOH HOH . G 7 HOH A 80 580 106 HOH HOH . G 7 HOH A 81 581 210 HOH HOH . G 7 HOH A 82 582 126 HOH HOH . G 7 HOH A 83 583 4 HOH HOH . G 7 HOH A 84 584 34 HOH HOH . G 7 HOH A 85 585 50 HOH HOH . G 7 HOH A 86 586 23 HOH HOH . G 7 HOH A 87 587 49 HOH HOH . G 7 HOH A 88 588 22 HOH HOH . G 7 HOH A 89 589 30 HOH HOH . G 7 HOH A 90 590 24 HOH HOH . G 7 HOH A 91 591 42 HOH HOH . G 7 HOH A 92 592 89 HOH HOH . G 7 HOH A 93 593 125 HOH HOH . G 7 HOH A 94 594 86 HOH HOH . G 7 HOH A 95 595 151 HOH HOH . G 7 HOH A 96 596 7 HOH HOH . G 7 HOH A 97 597 244 HOH HOH . G 7 HOH A 98 598 20 HOH HOH . G 7 HOH A 99 599 241 HOH HOH . G 7 HOH A 100 600 71 HOH HOH . G 7 HOH A 101 601 128 HOH HOH . G 7 HOH A 102 602 67 HOH HOH . G 7 HOH A 103 603 186 HOH HOH . G 7 HOH A 104 604 74 HOH HOH . G 7 HOH A 105 605 120 HOH HOH . G 7 HOH A 106 606 178 HOH HOH . G 7 HOH A 107 607 13 HOH HOH . G 7 HOH A 108 608 68 HOH HOH . G 7 HOH A 109 609 18 HOH HOH . G 7 HOH A 110 610 93 HOH HOH . G 7 HOH A 111 611 108 HOH HOH . G 7 HOH A 112 612 173 HOH HOH . G 7 HOH A 113 613 3 HOH HOH . G 7 HOH A 114 614 45 HOH HOH . G 7 HOH A 115 615 144 HOH HOH . G 7 HOH A 116 616 32 HOH HOH . G 7 HOH A 117 617 216 HOH HOH . G 7 HOH A 118 618 228 HOH HOH . G 7 HOH A 119 619 92 HOH HOH . G 7 HOH A 120 620 40 HOH HOH . G 7 HOH A 121 621 70 HOH HOH . G 7 HOH A 122 622 103 HOH HOH . G 7 HOH A 123 623 59 HOH HOH . G 7 HOH A 124 624 152 HOH HOH . G 7 HOH A 125 625 118 HOH HOH . G 7 HOH A 126 626 94 HOH HOH . G 7 HOH A 127 627 115 HOH HOH . G 7 HOH A 128 628 84 HOH HOH . G 7 HOH A 129 629 104 HOH HOH . G 7 HOH A 130 630 202 HOH HOH . G 7 HOH A 131 631 230 HOH HOH . G 7 HOH A 132 632 91 HOH HOH . G 7 HOH A 133 633 122 HOH HOH . G 7 HOH A 134 634 137 HOH HOH . G 7 HOH A 135 635 26 HOH HOH . G 7 HOH A 136 636 97 HOH HOH . G 7 HOH A 137 637 217 HOH HOH . G 7 HOH A 138 638 47 HOH HOH . G 7 HOH A 139 639 139 HOH HOH . G 7 HOH A 140 640 46 HOH HOH . G 7 HOH A 141 641 141 HOH HOH . G 7 HOH A 142 642 150 HOH HOH . G 7 HOH A 143 643 247 HOH HOH . G 7 HOH A 144 644 99 HOH HOH . G 7 HOH A 145 645 196 HOH HOH . G 7 HOH A 146 646 235 HOH HOH . G 7 HOH A 147 647 208 HOH HOH . G 7 HOH A 148 648 83 HOH HOH . G 7 HOH A 149 649 189 HOH HOH . G 7 HOH A 150 650 185 HOH HOH . G 7 HOH A 151 651 55 HOH HOH . G 7 HOH A 152 652 31 HOH HOH . G 7 HOH A 153 653 44 HOH HOH . G 7 HOH A 154 654 105 HOH HOH . G 7 HOH A 155 655 205 HOH HOH . G 7 HOH A 156 656 15 HOH HOH . G 7 HOH A 157 657 60 HOH HOH . G 7 HOH A 158 658 33 HOH HOH . G 7 HOH A 159 659 87 HOH HOH . G 7 HOH A 160 660 132 HOH HOH . G 7 HOH A 161 661 245 HOH HOH . G 7 HOH A 162 662 250 HOH HOH . G 7 HOH A 163 663 69 HOH HOH . G 7 HOH A 164 664 226 HOH HOH . G 7 HOH A 165 665 79 HOH HOH . G 7 HOH A 166 666 124 HOH HOH . G 7 HOH A 167 667 88 HOH HOH . G 7 HOH A 168 668 133 HOH HOH . G 7 HOH A 169 669 190 HOH HOH . G 7 HOH A 170 670 174 HOH HOH . G 7 HOH A 171 671 239 HOH HOH . G 7 HOH A 172 672 242 HOH HOH . G 7 HOH A 173 673 16 HOH HOH . G 7 HOH A 174 674 100 HOH HOH . G 7 HOH A 175 675 183 HOH HOH . G 7 HOH A 176 676 220 HOH HOH . G 7 HOH A 177 677 214 HOH HOH . G 7 HOH A 178 678 121 HOH HOH . G 7 HOH A 179 679 107 HOH HOH . G 7 HOH A 180 680 167 HOH HOH . G 7 HOH A 181 681 119 HOH HOH . G 7 HOH A 182 682 134 HOH HOH . G 7 HOH A 183 683 82 HOH HOH . G 7 HOH A 184 684 153 HOH HOH . G 7 HOH A 185 685 170 HOH HOH . G 7 HOH A 186 686 127 HOH HOH . G 7 HOH A 187 687 240 HOH HOH . G 7 HOH A 188 688 248 HOH HOH . G 7 HOH A 189 689 38 HOH HOH . G 7 HOH A 190 690 207 HOH HOH . G 7 HOH A 191 691 165 HOH HOH . G 7 HOH A 192 692 177 HOH HOH . G 7 HOH A 193 693 130 HOH HOH . G 7 HOH A 194 694 246 HOH HOH . G 7 HOH A 195 695 169 HOH HOH . G 7 HOH A 196 696 116 HOH HOH . G 7 HOH A 197 697 179 HOH HOH . G 7 HOH A 198 698 188 HOH HOH . G 7 HOH A 199 699 224 HOH HOH . G 7 HOH A 200 700 85 HOH HOH . G 7 HOH A 201 701 201 HOH HOH . G 7 HOH A 202 702 199 HOH HOH . G 7 HOH A 203 703 187 HOH HOH . G 7 HOH A 204 704 192 HOH HOH . G 7 HOH A 205 705 229 HOH HOH . G 7 HOH A 206 706 195 HOH HOH . G 7 HOH A 207 707 184 HOH HOH . G 7 HOH A 208 708 203 HOH HOH . G 7 HOH A 209 709 148 HOH HOH . G 7 HOH A 210 710 111 HOH HOH . G 7 HOH A 211 711 212 HOH HOH . G 7 HOH A 212 712 182 HOH HOH . G 7 HOH A 213 713 136 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 . . . B 2 60.703 8.772 24.818 1 61.39 ? O4 DST 401 A 1 HETATM 2 P P1 DST . . . B 2 61.768 7.763 25.178 1 60.43 ? P1 DST 401 A 1 HETATM 3 O O6 DST . . . B 2 61.865 7.637 26.682 1 68.32 ? O6 DST 401 A 1 HETATM 4 O O5 DST . . . B 2 63.114 8.203 24.646 1 74.1 ? O5 DST 401 A 1 HETATM 5 O O2 DST . . . B 2 61.353 6.315 24.502 1 62.96 ? O2 DST 401 A 1 HETATM 6 P P3 DST . . . B 2 62.28 4.947 24.607 1 102.04 ? P3 DST 401 A 1 HETATM 7 O O8 DST . . . B 2 61.537 3.894 25.43 1 42.32 ? O8 DST 401 A 1 HETATM 8 O O7 DST . . . B 2 63.601 5.317 25.291 1 74.67 ? O7 DST 401 A 1 HETATM 9 S S9 DST . . . B 2 62.615 4.217 22.623 1 57.75 ? S9 DST 401 A 1 HETATM 10 C C10 DST . . . B 2 61.993 2.509 22.56 1 35.42 ? C10 DST 401 A 1 HETATM 11 C C11 DST . . . B 2 63.054 1.443 22.313 1 27.88 ? C11 DST 401 A 1 HETATM 12 C C12 DST . . . B 2 63.889 1.52 21.301 1 34.17 ? C12 DST 401 A 1 HETATM 13 C C13 DST . . . B 2 63.854 2.683 20.308 1 37.79 ? C13 DST 401 A 1 HETATM 14 C C14 DST . . . B 2 64.907 0.398 21.132 1 35.2 ? C14 DST 401 A 1 HETATM 15 H H101 DST . . . B 2 61.563 2.314 23.408 1 42.65 ? H101 DST 401 A 1 HETATM 16 H H102 DST . . . B 2 61.339 2.453 21.846 1 42.65 ? H102 DST 401 A 1 HETATM 17 H H111 DST . . . B 2 63.112 0.719 22.893 1 33.6 ? H111 DST 401 A 1 HETATM 18 H H131 DST . . . B 2 64.127 2.369 19.432 1 45.49 ? H131 DST 401 A 1 HETATM 19 H H132 DST . . . B 2 64.461 3.38 20.605 1 45.49 ? H132 DST 401 A 1 HETATM 20 H H133 DST . . . B 2 62.953 3.039 20.258 1 45.49 ? H133 DST 401 A 1 HETATM 21 H H141 DST . . . B 2 64.451 -0.415 20.86 1 42.39 ? H141 DST 401 A 1 HETATM 22 H H142 DST . . . B 2 65.554 0.647 20.453 1 42.39 ? H142 DST 401 A 1 HETATM 23 H H143 DST . . . B 2 65.364 0.246 21.974 1 42.39 ? H143 DST 401 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 23 #