data_8DAY # _model_server_result.job_id AMm81DOitzKd2sLdnLXMww _model_server_result.datetime_utc '2025-01-10 18:15:10' _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 8day # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 8DAY # _exptl.entry_id 8DAY _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 8DAY _cell.length_a 90.066 _cell.length_b 107.717 _cell.length_c 180.722 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DAY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G 1 1 B,H 2 1 C,I 3 1 D,J 4 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 F _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 8DAY _atom_sites.fract_transf_matrix[1][1] 0.011103 _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] 0.009284 _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] 0.005533 _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 E 2 TYR A 1 501 501 TYR LTY . F 3 DST A 1 502 502 DST DST . G 4 HOH A 1 601 10 HOH HOH . G 4 HOH A 2 602 37 HOH HOH . G 4 HOH A 3 603 29 HOH HOH . G 4 HOH A 4 604 12 HOH HOH . G 4 HOH A 5 605 30 HOH HOH . G 4 HOH A 6 606 7 HOH HOH . G 4 HOH A 7 607 8 HOH HOH . G 4 HOH A 8 608 19 HOH HOH . G 4 HOH A 9 609 20 HOH HOH . G 4 HOH A 10 610 28 HOH HOH . G 4 HOH A 11 611 31 HOH HOH . G 4 HOH A 12 612 33 HOH HOH . G 4 HOH A 13 613 5 HOH HOH . G 4 HOH A 14 614 41 HOH HOH . G 4 HOH A 15 615 46 HOH HOH . G 4 HOH A 16 616 16 HOH HOH . G 4 HOH A 17 617 40 HOH HOH . G 4 HOH A 18 618 22 HOH HOH . G 4 HOH A 19 619 52 HOH HOH . G 4 HOH A 20 620 47 HOH HOH . G 4 HOH A 21 621 43 HOH HOH . G 4 HOH A 22 622 6 HOH HOH . G 4 HOH A 23 623 3 HOH HOH . G 4 HOH A 24 624 34 HOH HOH . G 4 HOH A 25 625 9 HOH HOH . G 4 HOH A 26 626 25 HOH HOH . G 4 HOH A 27 627 45 HOH HOH . G 4 HOH A 28 628 49 HOH HOH . G 4 HOH A 29 629 36 HOH HOH . G 4 HOH A 30 630 51 HOH HOH . H 4 HOH B 1 501 24 HOH HOH . H 4 HOH B 2 502 21 HOH HOH . H 4 HOH B 3 503 26 HOH HOH . H 4 HOH B 4 504 38 HOH HOH . H 4 HOH B 5 505 27 HOH HOH . H 4 HOH B 6 506 23 HOH HOH . H 4 HOH B 7 507 14 HOH HOH . H 4 HOH B 8 508 15 HOH HOH . H 4 HOH B 9 509 4 HOH HOH . H 4 HOH B 10 510 42 HOH HOH . H 4 HOH B 11 511 50 HOH HOH . I 4 HOH C 1 501 1 HOH HOH . I 4 HOH C 2 502 11 HOH HOH . I 4 HOH C 3 503 44 HOH HOH . I 4 HOH C 4 504 18 HOH HOH . I 4 HOH C 5 505 17 HOH HOH . J 4 HOH D 1 501 39 HOH HOH . J 4 HOH D 2 502 2 HOH HOH . J 4 HOH D 3 503 13 HOH HOH . J 4 HOH D 4 504 35 HOH HOH . J 4 HOH D 5 505 32 HOH HOH . J 4 HOH D 6 506 48 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 3 -21.693 -71.797 -64.374 0.62 94.27 -1 O4 DST 502 A 1 HETATM 2 P P1 DST . . . F 3 -22.475 -70.724 -65.098 0.62 90.61 ? P1 DST 502 A 1 HETATM 3 O O6 DST . . . F 3 -23.735 -70.418 -64.319 0.62 89.87 -1 O6 DST 502 A 1 HETATM 4 O O5 DST . . . F 3 -21.636 -69.474 -65.195 0.62 81.34 ? O5 DST 502 A 1 HETATM 5 O O2 DST . . . F 3 -22.849 -71.252 -66.619 0.62 96.4 ? O2 DST 502 A 1 HETATM 6 P P3 DST . . . F 3 -22.023 -70.773 -67.966 0.62 91.92 ? P3 DST 502 A 1 HETATM 7 O O8 DST . . . F 3 -20.539 -70.841 -67.695 0.62 94.23 ? O8 DST 502 A 1 HETATM 8 O O7 DST . . . F 3 -22.409 -69.35 -68.299 0.62 93.74 -1 O7 DST 502 A 1 HETATM 9 S S9 DST . . . F 3 -22.472 -72.001 -69.638 0.62 77.68 ? S9 DST 502 A 1 HETATM 10 C C10 DST . . . F 3 -21.574 -71.353 -71.079 0.62 64.33 ? C10 DST 502 A 1 HETATM 11 C C11 DST . . . F 3 -22.141 -69.972 -71.385 0.62 52.72 ? C11 DST 502 A 1 HETATM 12 C C12 DST . . . F 3 -21.572 -69.116 -72.2 0.62 47.77 ? C12 DST 502 A 1 HETATM 13 C C13 DST . . . F 3 -22.223 -67.756 -72.434 0.62 41.2 ? C13 DST 502 A 1 HETATM 14 C C14 DST . . . F 3 -20.273 -69.469 -72.906 0.62 63.81 ? C14 DST 502 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #