data_6VYA # _model_server_result.job_id C5jM-8beUUwxvsjMzldLJA _model_server_result.datetime_utc '2024-11-05 14:42:42' _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 6vya # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"ZA","auth_seq_id":502}' # _entry.id 6VYA # _exptl.entry_id 6VYA _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 24 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 78.255 _cell.angle_beta 65.051 _cell.angle_gamma 66.396 _cell.entry_id 6VYA _cell.length_a 157.893 _cell.length_b 163.069 _cell.length_c 167.857 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VYA _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 ? tetrameric 4 author_defined_assembly 3 ? tetrameric 4 author_defined_assembly 4 ? tetrameric 4 author_defined_assembly 5 ? tetrameric 4 author_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,Y,Z,AA,BA,EA,FA,GA,HA 1 1 C,V,W,X,CA,DA,OB,PB,QB,RB,SB,TB 2 1 F,G,H,I,IA,JA,KA,LA,MA,NA,OA,PA 3 1 J,K,L,M,QA,RA,SA,TA,UA,VA,WA,XA 4 1 N,O,P,Q,YA,ZA,AB,BB,CB,DB,EB,FB 5 1 R,S,T,U,GB,HB,IB,JB,KB,LB,MB,NB 6 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 ? 3 Z N N ? 3 BA N N ? 3 DA N N ? 3 FA N N ? 3 HA N N ? 3 JA N N ? 3 LA N N ? 3 NA N N ? 3 PA N N ? 3 RA N N ? 3 TA N N ? 3 VA N N ? 3 XA N N ? 3 ZA N N ? 3 BB N N ? 3 DB N N ? 3 FB N N ? 3 HB N N ? 3 JB N N ? 3 LB N N ? 3 NB N N ? 3 PB N N ? 3 RB N N ? 3 TB 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 6VYA _atom_sites.fract_transf_matrix[1][1] 0.006333 _atom_sites.fract_transf_matrix[1][2] -0.002768 _atom_sites.fract_transf_matrix[1][3] -0.002833 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006692 _atom_sites.fract_transf_matrix[2][3] -0.000279 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006576 _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 Y 2 QRP C 1 501 501 QRP QRP . Z 3 DST C 1 502 601 DST DST . AA 2 QRP A 1 501 501 QRP QRP . BA 3 DST A 1 502 601 DST DST . CA 2 QRP V 1 501 501 QRP QRP . DA 3 DST V 1 502 601 DST DST . EA 2 QRP E 1 501 501 QRP QRP . FA 3 DST E 1 502 601 DST DST . GA 2 QRP G 1 501 501 QRP QRP . HA 3 DST G 1 502 601 DST DST . IA 2 QRP B 1 501 501 QRP QRP . JA 3 DST B 1 502 601 DST DST . KA 2 QRP D 1 501 501 QRP QRP . LA 3 DST D 1 502 601 DST DST . MA 2 QRP F 1 501 501 QRP QRP . NA 3 DST F 1 502 601 DST DST . OA 2 QRP H 1 501 501 QRP QRP . PA 3 DST H 1 502 601 DST DST . QA 2 QRP I 1 501 501 QRP QRP . RA 3 DST I 1 502 601 DST DST . SA 2 QRP J 1 501 501 QRP QRP . TA 3 DST J 1 502 601 DST DST . UA 2 QRP K 1 501 501 QRP QRP . VA 3 DST K 1 502 601 DST DST . WA 2 QRP L 1 501 501 QRP QRP . XA 3 DST L 1 502 601 DST DST . YA 2 QRP M 1 501 501 QRP QRP . ZA 3 DST M 1 502 601 DST DST . AB 2 QRP N 1 501 501 QRP QRP . BB 3 DST N 1 502 601 DST DST . CB 2 QRP O 1 501 501 QRP QRP . DB 3 DST O 1 502 601 DST DST . EB 2 QRP P 1 501 501 QRP QRP . FB 3 DST P 1 502 601 DST DST . GB 2 QRP Q 1 501 501 QRP QRP . HB 3 DST Q 1 502 601 DST DST . IB 2 QRP R 1 501 501 QRP QRP . JB 3 DST R 1 502 601 DST DST . KB 2 QRP S 1 501 501 QRP QRP . LB 3 DST S 1 502 601 DST DST . MB 2 QRP T 1 501 501 QRP QRP . NB 3 DST T 1 502 601 DST DST . OB 2 QRP U 1 501 501 QRP QRP . PB 3 DST U 1 502 601 DST DST . QB 2 QRP W 1 501 501 QRP QRP . RB 3 DST W 1 502 601 DST DST . SB 2 QRP X 1 501 501 QRP QRP . TB 3 DST X 1 502 601 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 . . . ZA 3 49.619 107.895 -9.706 1 131.75 ? O4 DST 502 M 1 HETATM 2 P P1 DST . . . ZA 3 48.977 106.83 -8.928 1 164.63 ? P1 DST 502 M 1 HETATM 3 O O6 DST . . . ZA 3 48.311 107.437 -7.739 1 118.13 ? O6 DST 502 M 1 HETATM 4 O O5 DST . . . ZA 3 48.159 106.035 -9.875 1 145.07 ? O5 DST 502 M 1 HETATM 5 O O2 DST . . . ZA 3 50.143 105.853 -8.37 1 124.49 ? O2 DST 502 M 1 HETATM 6 P P3 DST . . . ZA 3 51.701 106.336 -8.196 1 133.34 ? P3 DST 502 M 1 HETATM 7 O O8 DST . . . ZA 3 51.795 107.281 -7.024 1 119.1 ? O8 DST 502 M 1 HETATM 8 O O7 DST . . . ZA 3 52.073 107.081 -9.443 1 125.47 ? O7 DST 502 M 1 HETATM 9 S S9 DST . . . ZA 3 53.083 104.761 -7.878 1 93.62 ? S9 DST 502 M 1 HETATM 10 C C10 DST . . . ZA 3 54.757 105.48 -7.901 1 113.16 ? C10 DST 502 M 1 HETATM 11 C C11 DST . . . ZA 3 55.626 104.573 -8.762 1 118.08 ? C11 DST 502 M 1 HETATM 12 C C12 DST . . . ZA 3 56.958 104.648 -8.76 1 115.94 ? C12 DST 502 M 1 HETATM 13 C C13 DST . . . ZA 3 57.718 103.68 -9.708 1 119.91 ? C13 DST 502 M 1 HETATM 14 C C14 DST . . . ZA 3 57.738 105.598 -7.799 1 101.16 ? C14 DST 502 M 1 HETATM 15 H H101 DST . . . ZA 3 55.155 105.528 -6.893 1 135.55 ? H101 DST 502 M 1 HETATM 16 H H102 DST . . . ZA 3 54.727 106.478 -8.325 1 135.55 ? H102 DST 502 M 1 HETATM 17 H H111 DST . . . ZA 3 55.146 103.841 -9.399 1 141.45 ? H111 DST 502 M 1 HETATM 18 H H131 DST . . . ZA 3 57.871 102.729 -9.206 1 143.64 ? H131 DST 502 M 1 HETATM 19 H H132 DST . . . ZA 3 58.68 104.11 -9.969 1 143.64 ? H132 DST 502 M 1 HETATM 20 H H133 DST . . . ZA 3 57.134 103.524 -10.61 1 143.64 ? H133 DST 502 M 1 HETATM 21 H H141 DST . . . ZA 3 57.315 106.596 -7.855 1 121.14 ? H141 DST 502 M 1 HETATM 22 H H142 DST . . . ZA 3 57.658 105.228 -6.781 1 121.14 ? H142 DST 502 M 1 HETATM 23 H H143 DST . . . ZA 3 58.783 105.631 -8.092 1 121.14 ? H143 DST 502 M 1 # _model_server_stats.io_time_ms 99 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 453 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 23 #