data_5TU6 # _model_server_result.job_id 83HOPMIlFSPrxA75LFN1Aw _model_server_result.datetime_utc '2024-11-23 20:27:00' _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 5tu6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":404}' # _entry.id 5TU6 # _exptl.entry_id 5TU6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 262.158 _entity.id 5 _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 5TU6 _cell.length_a 116.49 _cell.length_b 116.49 _cell.length_c 43.58 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TU6 _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,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 5 _struct_asym.id F _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 A OD1 ASP 125 A ASP 125 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc2 A OE1 GLU 184 A GLU 184 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 C MG MG . A MG 401 1_555 F O7 DST . A DST 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc4 C MG MG . A MG 401 1_555 F O5 DST . A DST 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc5 C MG MG . A MG 401 1_555 G O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc7 C MG MG . A MG 401 1_555 G O HOH . A HOH 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc8 D MG MG . A MG 402 1_555 F O6 DST . A DST 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc9 D MG MG . A MG 402 1_555 G O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc10 D MG MG . A MG 402 1_555 G O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc11 D MG MG . A MG 402 1_555 G O HOH . A HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc12 D MG MG . A MG 402 1_555 G O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? # _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 5TU6 _atom_sites.fract_transf_matrix[1][1] 0.008584 _atom_sites.fract_transf_matrix[1][2] 0.004956 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009912 _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] 0.022946 _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 MG A 1 401 301 MG MG . D 3 MG A 1 402 302 MG MG . E 4 MET A 1 403 297 MET MET . F 5 DST A 1 404 300 DST DST . G 6 HOH A 1 501 156 HOH HOH . G 6 HOH A 2 502 12 HOH HOH . G 6 HOH A 3 503 94 HOH HOH . G 6 HOH A 4 504 27 HOH HOH . G 6 HOH A 5 505 35 HOH HOH . G 6 HOH A 6 506 158 HOH HOH . G 6 HOH A 7 507 116 HOH HOH . G 6 HOH A 8 508 128 HOH HOH . G 6 HOH A 9 509 49 HOH HOH . G 6 HOH A 10 510 99 HOH HOH . G 6 HOH A 11 511 161 HOH HOH . G 6 HOH A 12 512 151 HOH HOH . G 6 HOH A 13 513 59 HOH HOH . G 6 HOH A 14 514 5 HOH HOH . G 6 HOH A 15 515 88 HOH HOH . G 6 HOH A 16 516 53 HOH HOH . G 6 HOH A 17 517 4 HOH HOH . G 6 HOH A 18 518 86 HOH HOH . G 6 HOH A 19 519 18 HOH HOH . G 6 HOH A 20 520 38 HOH HOH . G 6 HOH A 21 521 51 HOH HOH . G 6 HOH A 22 522 66 HOH HOH . G 6 HOH A 23 523 164 HOH HOH . G 6 HOH A 24 524 10 HOH HOH . G 6 HOH A 25 525 54 HOH HOH . G 6 HOH A 26 526 61 HOH HOH . G 6 HOH A 27 527 85 HOH HOH . G 6 HOH A 28 528 152 HOH HOH . G 6 HOH A 29 529 155 HOH HOH . G 6 HOH A 30 530 112 HOH HOH . G 6 HOH A 31 531 153 HOH HOH . G 6 HOH A 32 532 31 HOH HOH . G 6 HOH A 33 533 73 HOH HOH . G 6 HOH A 34 534 58 HOH HOH . G 6 HOH A 35 535 110 HOH HOH . G 6 HOH A 36 536 3 HOH HOH . G 6 HOH A 37 537 149 HOH HOH . G 6 HOH A 38 538 62 HOH HOH . G 6 HOH A 39 539 139 HOH HOH . G 6 HOH A 40 540 83 HOH HOH . G 6 HOH A 41 541 29 HOH HOH . G 6 HOH A 42 542 57 HOH HOH . G 6 HOH A 43 543 160 HOH HOH . G 6 HOH A 44 544 16 HOH HOH . G 6 HOH A 45 545 46 HOH HOH . G 6 HOH A 46 546 65 HOH HOH . G 6 HOH A 47 547 7 HOH HOH . G 6 HOH A 48 548 67 HOH HOH . G 6 HOH A 49 549 105 HOH HOH . G 6 HOH A 50 550 104 HOH HOH . G 6 HOH A 51 551 34 HOH HOH . G 6 HOH A 52 552 126 HOH HOH . G 6 HOH A 53 553 13 HOH HOH . G 6 HOH A 54 554 72 HOH HOH . G 6 HOH A 55 555 107 HOH HOH . G 6 HOH A 56 556 127 HOH HOH . G 6 HOH A 57 557 78 HOH HOH . G 6 HOH A 58 558 148 HOH HOH . G 6 HOH A 59 559 75 HOH HOH . G 6 HOH A 60 560 56 HOH HOH . G 6 HOH A 61 561 70 HOH HOH . G 6 HOH A 62 562 154 HOH HOH . G 6 HOH A 63 563 81 HOH HOH . G 6 HOH A 64 564 90 HOH HOH . G 6 HOH A 65 565 123 HOH HOH . G 6 HOH A 66 566 74 HOH HOH . G 6 HOH A 67 567 109 HOH HOH . G 6 HOH A 68 568 21 HOH HOH . G 6 HOH A 69 569 97 HOH HOH . G 6 HOH A 70 570 92 HOH HOH . G 6 HOH A 71 571 71 HOH HOH . G 6 HOH A 72 572 64 HOH HOH . G 6 HOH A 73 573 101 HOH HOH . G 6 HOH A 74 574 103 HOH HOH . G 6 HOH A 75 575 119 HOH HOH . G 6 HOH A 76 576 19 HOH HOH . G 6 HOH A 77 577 117 HOH HOH . G 6 HOH A 78 578 162 HOH HOH . G 6 HOH A 79 579 163 HOH HOH . G 6 HOH A 80 580 20 HOH HOH . G 6 HOH A 81 581 17 HOH HOH . G 6 HOH A 82 582 50 HOH HOH . G 6 HOH A 83 583 89 HOH HOH . G 6 HOH A 84 584 150 HOH HOH . G 6 HOH A 85 585 69 HOH HOH . G 6 HOH A 86 586 47 HOH HOH . G 6 HOH A 87 587 142 HOH HOH . G 6 HOH A 88 588 125 HOH HOH . G 6 HOH A 89 589 133 HOH HOH . G 6 HOH A 90 590 33 HOH HOH . G 6 HOH A 91 591 141 HOH HOH . G 6 HOH A 92 592 102 HOH HOH . G 6 HOH A 93 593 135 HOH HOH . G 6 HOH A 94 594 24 HOH HOH . G 6 HOH A 95 595 136 HOH HOH . G 6 HOH A 96 596 91 HOH HOH . G 6 HOH A 97 597 113 HOH HOH . G 6 HOH A 98 598 6 HOH HOH . G 6 HOH A 99 599 68 HOH HOH . G 6 HOH A 100 600 26 HOH HOH . G 6 HOH A 101 601 87 HOH HOH . G 6 HOH A 102 602 118 HOH HOH . G 6 HOH A 103 603 159 HOH HOH . G 6 HOH A 104 604 106 HOH HOH . G 6 HOH A 105 605 115 HOH HOH . G 6 HOH A 106 606 120 HOH HOH . G 6 HOH A 107 607 121 HOH HOH . G 6 HOH A 108 608 157 HOH HOH . G 6 HOH A 109 609 79 HOH HOH . G 6 HOH A 110 610 80 HOH HOH . G 6 HOH A 111 611 122 HOH HOH . G 6 HOH A 112 612 111 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 . . . F 5 15.508 93.668 -2.224 1 46.75 ? O4 DST 404 A 1 HETATM 2 P P1 DST . . . F 5 15.438 92.665 -3.329 1 42.38 ? P1 DST 404 A 1 HETATM 3 O O6 DST . . . F 5 14.178 92.853 -4.144 1 44.27 ? O6 DST 404 A 1 HETATM 4 O O5 DST . . . F 5 16.688 92.739 -4.166 1 40.02 ? O5 DST 404 A 1 HETATM 5 O O2 DST . . . F 5 15.208 91.252 -2.635 1 40.79 ? O2 DST 404 A 1 HETATM 6 P P3 DST . . . F 5 16.118 89.944 -2.747 1 38.26 ? P3 DST 404 A 1 HETATM 7 O O8 DST . . . F 5 15.263 88.819 -3.269 1 39.98 ? O8 DST 404 A 1 HETATM 8 O O7 DST . . . F 5 17.407 90.099 -3.504 1 37.15 ? O7 DST 404 A 1 HETATM 9 S S9 DST . . . F 5 16.535 89.544 -0.811 1 45.98 ? S9 DST 404 A 1 HETATM 10 C C10 DST . . . F 5 16.11 87.866 -0.509 1 43.27 ? C10 DST 404 A 1 HETATM 11 C C11 DST . . . F 5 17.213 87.351 0.379 1 42.56 ? C11 DST 404 A 1 HETATM 12 C C12 DST . . . F 5 17.259 87.567 1.696 1 42.79 ? C12 DST 404 A 1 HETATM 13 C C13 DST . . . F 5 16.227 88.314 2.5 1 45.04 ? C13 DST 404 A 1 HETATM 14 C C14 DST . . . F 5 18.428 87.01 2.411 1 46.53 ? C14 DST 404 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #