data_8X37 # _model_server_result.job_id M4io6e2-Axn1YgcuiQl5Bg _model_server_result.datetime_utc '2024-12-21 16:19:45' _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 8x37 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8X37 # _exptl.entry_id 8X37 _exptl.method 'X-RAY DIFFRACTION' # _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 91.327 _cell.angle_gamma 90 _cell.entry_id 8X37 _cell.length_a 98.26 _cell.length_b 50.27 _cell.length_c 120.25 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X37 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,H,I,J,K _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 C N N ? 2 D N N ? 2 F N N ? 2 G N 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 disulf ? disulf1 A SG CYS 13 A CYS 54 1_555 B SG CYS 127 B CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 23 A CYS 64 1_555 A SG CYS 200 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf3 A SG CYS 127 A CYS 168 1_555 B SG CYS 13 B CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 B SG CYS 23 B CYS 64 1_555 B SG CYS 200 B CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc1 A OD1 ASP 45 A ASP 86 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc2 C O4 DST . A DST 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc3 C O7 DST . A DST 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc4 D O7 DST . A DST 402 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc5 B OD1 ASP 45 B ASP 86 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc6 F O6 DST . B DST 401 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc7 F O7 DST . B DST 401 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc8 G O7 DST . B DST 402 1_555 H MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? # _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 8X37 _atom_sites.fract_transf_matrix[1][1] 0.010177 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000236 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019893 _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] 0.008318 _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 2 DST A 1 401 401 DST DST . D 2 DST A 1 402 501 DST DST . E 3 MG A 1 403 601 MG MG . F 2 DST B 1 401 401 DST DST . G 2 DST B 1 402 501 DST DST . H 3 MG B 1 403 601 MG MG . I 3 MG B 1 404 701 MG MG . J 4 HOH A 1 501 13 HOH HOH . J 4 HOH A 2 502 46 HOH HOH . J 4 HOH A 3 503 43 HOH HOH . J 4 HOH A 4 504 44 HOH HOH . J 4 HOH A 5 505 38 HOH HOH . J 4 HOH A 6 506 39 HOH HOH . J 4 HOH A 7 507 30 HOH HOH . J 4 HOH A 8 508 25 HOH HOH . J 4 HOH A 9 509 10 HOH HOH . J 4 HOH A 10 510 40 HOH HOH . J 4 HOH A 11 511 24 HOH HOH . J 4 HOH A 12 512 21 HOH HOH . J 4 HOH A 13 513 35 HOH HOH . J 4 HOH A 14 514 6 HOH HOH . J 4 HOH A 15 515 1 HOH HOH . J 4 HOH A 16 516 7 HOH HOH . J 4 HOH A 17 517 9 HOH HOH . J 4 HOH A 18 518 23 HOH HOH . J 4 HOH A 19 519 2 HOH HOH . J 4 HOH A 20 520 3 HOH HOH . J 4 HOH A 21 521 34 HOH HOH . J 4 HOH A 22 522 31 HOH HOH . J 4 HOH A 23 523 14 HOH HOH . J 4 HOH A 24 524 32 HOH HOH . J 4 HOH A 25 525 45 HOH HOH . K 4 HOH B 1 501 36 HOH HOH . K 4 HOH B 2 502 47 HOH HOH . K 4 HOH B 3 503 19 HOH HOH . K 4 HOH B 4 504 8 HOH HOH . K 4 HOH B 5 505 17 HOH HOH . K 4 HOH B 6 506 37 HOH HOH . K 4 HOH B 7 507 26 HOH HOH . K 4 HOH B 8 508 16 HOH HOH . K 4 HOH B 9 509 20 HOH HOH . K 4 HOH B 10 510 29 HOH HOH . K 4 HOH B 11 511 42 HOH HOH . K 4 HOH B 12 512 27 HOH HOH . K 4 HOH B 13 513 11 HOH HOH . K 4 HOH B 14 514 4 HOH HOH . K 4 HOH B 15 515 18 HOH HOH . K 4 HOH B 16 516 33 HOH HOH . K 4 HOH B 17 517 22 HOH HOH . K 4 HOH B 18 518 5 HOH HOH . K 4 HOH B 19 519 15 HOH HOH . K 4 HOH B 20 520 12 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 2 24.157 11.262 19.008 1 57.09 0 O4 DST 401 A 1 HETATM 2 P P1 DST . . . C 2 24.822 12.168 18.031 1 60.23 0 P1 DST 401 A 1 HETATM 3 O O6 DST . . . C 2 26.242 11.791 17.782 1 61.38 0 O6 DST 401 A 1 HETATM 4 O O5 DST . . . C 2 24.619 13.623 18.351 1 55.27 0 O5 DST 401 A 1 HETATM 5 O O2 DST . . . C 2 24.119 11.859 16.642 1 56.38 0 O2 DST 401 A 1 HETATM 6 P P3 DST . . . C 2 22.595 11.628 16.254 1 64 0 P3 DST 401 A 1 HETATM 7 O O8 DST . . . C 2 22.243 12.566 15.144 1 78.36 0 O8 DST 401 A 1 HETATM 8 O O7 DST . . . C 2 21.759 11.594 17.501 1 69.18 0 O7 DST 401 A 1 HETATM 9 S S9 DST . . . C 2 22.585 9.693 15.677 1 73.88 0 S9 DST 401 A 1 HETATM 10 C C10 DST . . . C 2 20.893 9.254 16.165 1 89.37 0 C10 DST 401 A 1 HETATM 11 C C11 DST . . . C 2 20.265 8.435 15.114 1 89.53 0 C11 DST 401 A 1 HETATM 12 C C12 DST . . . C 2 19.559 8.891 14.093 1 92.51 0 C12 DST 401 A 1 HETATM 13 C C13 DST . . . C 2 19.135 10.328 13.942 1 85.07 0 C13 DST 401 A 1 HETATM 14 C C14 DST . . . C 2 19.165 7.991 12.958 1 91.58 0 C14 DST 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #