data_9JHX # _model_server_result.job_id xSYdPld6T_D5jx0Bpumcdw _model_server_result.datetime_utc '2025-03-13 06:40:49' _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 9jhx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 9JHX # _exptl.entry_id 9JHX _exptl.method 'ELECTRON MICROSCOPY' # _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 4 _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 9JHX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JHX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N 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 9JHX _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 DST A 1 501 501 DST DST . F 2 DST B 1 501 501 DST DST . G 2 DST C 1 501 501 DST DST . H 2 DST D 1 501 501 DST DST . # 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 . . . H 2 138.026 126.793 139.74 1 70.35 ? O4 DST 501 D 1 HETATM 2 P P1 DST . . . H 2 137.505 125.627 139.044 1 70.35 ? P1 DST 501 D 1 HETATM 3 O O6 DST . . . H 2 138.312 125.535 137.839 1 70.35 ? O6 DST 501 D 1 HETATM 4 O O5 DST . . . H 2 137.926 124.499 139.862 1 70.35 ? O5 DST 501 D 1 HETATM 5 O O2 DST . . . H 2 135.899 125.71 138.738 1 70.35 ? O2 DST 501 D 1 HETATM 6 P P3 DST . . . H 2 135.231 127.079 138.131 1 70.35 ? P3 DST 501 D 1 HETATM 7 O O8 DST . . . H 2 135.976 127.474 136.881 1 70.35 ? O8 DST 501 D 1 HETATM 8 O O7 DST . . . H 2 135.353 128.181 139.15 1 70.35 ? O7 DST 501 D 1 HETATM 9 S S9 DST . . . H 2 133.193 126.733 137.664 1 70.35 ? S9 DST 501 D 1 HETATM 10 C C10 DST . . . H 2 132.211 126.996 139.164 1 70.35 ? C10 DST 501 D 1 HETATM 11 C C11 DST . . . H 2 130.738 127.034 138.788 1 70.35 ? C11 DST 501 D 1 HETATM 12 C C12 DST . . . H 2 130.205 125.612 138.76 1 70.35 ? C12 DST 501 D 1 HETATM 13 C C13 DST . . . H 2 130.6 124.876 140.034 1 70.35 ? C13 DST 501 D 1 HETATM 14 C C14 DST . . . H 2 128.691 125.662 138.642 1 70.35 ? C14 DST 501 D 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #