data_5TU5 # _model_server_result.job_id wbqiAQbgPVbQnuwvSpp-IQ _model_server_result.datetime_utc '2024-11-05 08:11:37' _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 5tu5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5TU5 # _exptl.entry_id 5TU5 _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 120 _cell.entry_id 5TU5 _cell.length_a 117.042 _cell.length_b 117.042 _cell.length_c 43.8 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TU5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 C O5 DST . A DST 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc2 C O7 DST . A DST 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc3 D MG MG . A MG 402 1_555 E O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc4 D MG MG . A MG 402 1_555 E O HOH . A HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? # _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 5TU5 _atom_sites.fract_transf_matrix[1][1] 0.008544 _atom_sites.fract_transf_matrix[1][2] 0.004933 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009866 _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] 0.022831 _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 3 DST A 1 401 400 DST DST . D 4 MG A 1 402 500 MG MG . E 5 HOH A 1 501 146 HOH HOH . E 5 HOH A 2 502 115 HOH HOH . E 5 HOH A 3 503 91 HOH HOH . E 5 HOH A 4 504 101 HOH HOH . E 5 HOH A 5 505 102 HOH HOH . E 5 HOH A 6 506 67 HOH HOH . E 5 HOH A 7 507 77 HOH HOH . E 5 HOH A 8 508 9 HOH HOH . E 5 HOH A 9 509 5 HOH HOH . E 5 HOH A 10 510 92 HOH HOH . E 5 HOH A 11 511 38 HOH HOH . E 5 HOH A 12 512 75 HOH HOH . E 5 HOH A 13 513 74 HOH HOH . E 5 HOH A 14 514 35 HOH HOH . E 5 HOH A 15 515 98 HOH HOH . E 5 HOH A 16 516 62 HOH HOH . E 5 HOH A 17 517 27 HOH HOH . E 5 HOH A 18 518 48 HOH HOH . E 5 HOH A 19 519 129 HOH HOH . E 5 HOH A 20 520 97 HOH HOH . E 5 HOH A 21 521 18 HOH HOH . E 5 HOH A 22 522 3 HOH HOH . E 5 HOH A 23 523 127 HOH HOH . E 5 HOH A 24 524 68 HOH HOH . E 5 HOH A 25 525 110 HOH HOH . E 5 HOH A 26 526 8 HOH HOH . E 5 HOH A 27 527 86 HOH HOH . E 5 HOH A 28 528 54 HOH HOH . E 5 HOH A 29 529 17 HOH HOH . E 5 HOH A 30 530 147 HOH HOH . E 5 HOH A 31 531 122 HOH HOH . E 5 HOH A 32 532 31 HOH HOH . E 5 HOH A 33 533 51 HOH HOH . E 5 HOH A 34 534 6 HOH HOH . E 5 HOH A 35 535 32 HOH HOH . E 5 HOH A 36 536 63 HOH HOH . E 5 HOH A 37 537 11 HOH HOH . E 5 HOH A 38 538 85 HOH HOH . E 5 HOH A 39 539 2 HOH HOH . E 5 HOH A 40 540 56 HOH HOH . E 5 HOH A 41 541 1 HOH HOH . E 5 HOH A 42 542 29 HOH HOH . E 5 HOH A 43 543 57 HOH HOH . E 5 HOH A 44 544 88 HOH HOH . E 5 HOH A 45 545 33 HOH HOH . E 5 HOH A 46 546 136 HOH HOH . E 5 HOH A 47 547 132 HOH HOH . E 5 HOH A 48 548 30 HOH HOH . E 5 HOH A 49 549 49 HOH HOH . E 5 HOH A 50 550 14 HOH HOH . E 5 HOH A 51 551 20 HOH HOH . E 5 HOH A 52 552 82 HOH HOH . E 5 HOH A 53 553 130 HOH HOH . E 5 HOH A 54 554 58 HOH HOH . E 5 HOH A 55 555 53 HOH HOH . E 5 HOH A 56 556 70 HOH HOH . E 5 HOH A 57 557 73 HOH HOH . E 5 HOH A 58 558 106 HOH HOH . E 5 HOH A 59 559 103 HOH HOH . E 5 HOH A 60 560 134 HOH HOH . E 5 HOH A 61 561 55 HOH HOH . E 5 HOH A 62 562 72 HOH HOH . E 5 HOH A 63 563 145 HOH HOH . E 5 HOH A 64 564 119 HOH HOH . E 5 HOH A 65 565 94 HOH HOH . E 5 HOH A 66 566 21 HOH HOH . E 5 HOH A 67 567 141 HOH HOH . E 5 HOH A 68 568 150 HOH HOH . E 5 HOH A 69 569 112 HOH HOH . E 5 HOH A 70 570 7 HOH HOH . E 5 HOH A 71 571 76 HOH HOH . E 5 HOH A 72 572 60 HOH HOH . E 5 HOH A 73 573 37 HOH HOH . E 5 HOH A 74 574 89 HOH HOH . E 5 HOH A 75 575 156 HOH HOH . E 5 HOH A 76 576 36 HOH HOH . E 5 HOH A 77 577 34 HOH HOH . E 5 HOH A 78 578 135 HOH HOH . E 5 HOH A 79 579 78 HOH HOH . E 5 HOH A 80 580 47 HOH HOH . E 5 HOH A 81 581 160 HOH HOH . E 5 HOH A 82 582 81 HOH HOH . E 5 HOH A 83 583 40 HOH HOH . E 5 HOH A 84 584 116 HOH HOH . E 5 HOH A 85 585 87 HOH HOH . E 5 HOH A 86 586 125 HOH HOH . E 5 HOH A 87 587 16 HOH HOH . E 5 HOH A 88 588 109 HOH HOH . E 5 HOH A 89 589 39 HOH HOH . E 5 HOH A 90 590 84 HOH HOH . E 5 HOH A 91 591 133 HOH HOH . E 5 HOH A 92 592 117 HOH HOH . E 5 HOH A 93 593 139 HOH HOH . E 5 HOH A 94 594 137 HOH HOH . E 5 HOH A 95 595 19 HOH HOH . E 5 HOH A 96 596 128 HOH HOH . E 5 HOH A 97 597 22 HOH HOH . E 5 HOH A 98 598 44 HOH HOH . E 5 HOH A 99 599 155 HOH HOH . E 5 HOH A 100 600 80 HOH HOH . E 5 HOH A 101 601 83 HOH HOH . E 5 HOH A 102 602 15 HOH HOH . E 5 HOH A 103 603 124 HOH HOH . E 5 HOH A 104 604 28 HOH HOH . E 5 HOH A 105 605 99 HOH HOH . E 5 HOH A 106 606 52 HOH HOH . E 5 HOH A 107 607 61 HOH HOH . E 5 HOH A 108 608 69 HOH HOH . E 5 HOH A 109 609 65 HOH HOH . E 5 HOH A 110 610 143 HOH HOH . E 5 HOH A 111 611 107 HOH HOH . E 5 HOH A 112 612 50 HOH HOH . E 5 HOH A 113 613 149 HOH HOH . E 5 HOH A 114 614 41 HOH HOH . E 5 HOH A 115 615 151 HOH HOH . E 5 HOH A 116 616 114 HOH HOH . E 5 HOH A 117 617 118 HOH HOH . E 5 HOH A 118 618 96 HOH HOH . E 5 HOH A 119 619 121 HOH HOH . E 5 HOH A 120 620 153 HOH HOH . E 5 HOH A 121 621 126 HOH HOH . E 5 HOH A 122 622 59 HOH HOH . E 5 HOH A 123 623 161 HOH HOH . E 5 HOH A 124 624 111 HOH HOH . E 5 HOH A 125 625 100 HOH HOH . E 5 HOH A 126 626 105 HOH HOH . E 5 HOH A 127 627 144 HOH HOH . E 5 HOH A 128 628 66 HOH HOH . E 5 HOH A 129 629 148 HOH HOH . E 5 HOH A 130 630 71 HOH HOH . E 5 HOH A 131 631 64 HOH HOH . E 5 HOH A 132 632 90 HOH HOH . E 5 HOH A 133 633 138 HOH HOH . E 5 HOH A 134 634 142 HOH HOH . E 5 HOH A 135 635 104 HOH HOH . E 5 HOH A 136 636 131 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 73.906 143.965 -4.699 1 27.45 ? O4 DST 401 A 1 HETATM 2 P P1 DST . . . C 3 72.834 143.087 -4.092 1 26.32 ? P1 DST 401 A 1 HETATM 3 O O6 DST . . . C 3 73.177 142.771 -2.658 1 27.3 ? O6 DST 401 A 1 HETATM 4 O O5 DST . . . C 3 72.624 141.821 -4.888 1 24.12 ? O5 DST 401 A 1 HETATM 5 O O2 DST . . . C 3 71.522 144.006 -4.105 1 27.62 ? O2 DST 401 A 1 HETATM 6 P P3 DST . . . C 3 70.023 143.496 -4.386 1 26.16 ? P3 DST 401 A 1 HETATM 7 O O8 DST . . . C 3 69.293 144.702 -4.904 1 26.75 ? O8 DST 401 A 1 HETATM 8 O O7 DST . . . C 3 69.933 142.386 -5.396 1 29.98 ? O7 DST 401 A 1 HETATM 9 S S9 DST . . . C 3 69.246 142.834 -2.622 1 31.35 ? S9 DST 401 A 1 HETATM 10 C C10 DST . . . C 3 68.833 144.283 -1.717 1 29.12 ? C10 DST 401 A 1 HETATM 11 C C11 DST . . . C 3 68.352 143.858 -0.347 1 29.33 ? C11 DST 401 A 1 HETATM 12 C C12 DST . . . C 3 67.095 143.478 -0.071 1 27.8 ? C12 DST 401 A 1 HETATM 13 C C13 DST . . . C 3 65.995 143.448 -1.088 1 28.32 ? C13 DST 401 A 1 HETATM 14 C C14 DST . . . C 3 66.768 143.076 1.323 1 27.98 ? C14 DST 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #