data_8X36 # _model_server_result.job_id C9iTHcbQhiDXQk4Q4z6E0A _model_server_result.datetime_utc '2024-12-22 01:33:13' _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 8x36 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8X36 # _exptl.entry_id 8X36 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.69 _cell.angle_gamma 90 _cell.entry_id 8X36 _cell.length_a 97.52 _cell.length_b 48.68 _cell.length_c 121.13 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X36 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _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 _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 H 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 23 A CYS 64 1_555 A SG CYS 200 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 127 A CYS 168 1_555 B SG CYS 13 B CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 B SG CYS 23 B CYS 64 1_555 B SG CYS 200 B CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc1 A OD1 ASP 45 A ASP 86 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc2 C O5 DST . A DST 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc3 C O8 DST . A DST 401 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 D O1A IPE . A IPE 402 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc5 B OD1 ASP 45 B ASP 86 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc6 F O2A IPE . B IPE 401 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc7 G MG MG . B MG 402 1_555 H O6 DST . B DST 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc8 G MG MG . B MG 402 1_555 H O8 DST . B DST 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? # _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 8X36 _atom_sites.fract_transf_matrix[1][1] 0.010254 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000123 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020542 _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] 0.008256 _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 3 IPE A 1 402 402 IPE IPE . E 4 MG A 1 403 403 MG MG . F 3 IPE B 1 401 401 IPE IPE . G 4 MG B 1 402 403 MG MG . H 2 DST B 1 403 404 DST DST . I 5 HOH A 1 501 89 HOH HOH . I 5 HOH A 2 502 35 HOH HOH . I 5 HOH A 3 503 83 HOH HOH . I 5 HOH A 4 504 10 HOH HOH . I 5 HOH A 5 505 5 HOH HOH . I 5 HOH A 6 506 15 HOH HOH . I 5 HOH A 7 507 75 HOH HOH . I 5 HOH A 8 508 59 HOH HOH . I 5 HOH A 9 509 61 HOH HOH . I 5 HOH A 10 510 49 HOH HOH . I 5 HOH A 11 511 7 HOH HOH . I 5 HOH A 12 512 13 HOH HOH . I 5 HOH A 13 513 3 HOH HOH . I 5 HOH A 14 514 76 HOH HOH . I 5 HOH A 15 515 52 HOH HOH . I 5 HOH A 16 516 86 HOH HOH . I 5 HOH A 17 517 4 HOH HOH . I 5 HOH A 18 518 1 HOH HOH . I 5 HOH A 19 519 62 HOH HOH . I 5 HOH A 20 520 25 HOH HOH . I 5 HOH A 21 521 66 HOH HOH . I 5 HOH A 22 522 67 HOH HOH . I 5 HOH A 23 523 73 HOH HOH . I 5 HOH A 24 524 42 HOH HOH . I 5 HOH A 25 525 81 HOH HOH . I 5 HOH A 26 526 46 HOH HOH . I 5 HOH A 27 527 9 HOH HOH . I 5 HOH A 28 528 33 HOH HOH . I 5 HOH A 29 529 68 HOH HOH . I 5 HOH A 30 530 64 HOH HOH . I 5 HOH A 31 531 48 HOH HOH . I 5 HOH A 32 532 31 HOH HOH . I 5 HOH A 33 533 69 HOH HOH . I 5 HOH A 34 534 74 HOH HOH . I 5 HOH A 35 535 11 HOH HOH . I 5 HOH A 36 536 32 HOH HOH . I 5 HOH A 37 537 53 HOH HOH . I 5 HOH A 38 538 47 HOH HOH . I 5 HOH A 39 539 71 HOH HOH . I 5 HOH A 40 540 41 HOH HOH . I 5 HOH A 41 541 36 HOH HOH . I 5 HOH A 42 542 24 HOH HOH . I 5 HOH A 43 543 85 HOH HOH . I 5 HOH A 44 544 30 HOH HOH . I 5 HOH A 45 545 78 HOH HOH . I 5 HOH A 46 546 87 HOH HOH . I 5 HOH A 47 547 29 HOH HOH . I 5 HOH A 48 548 65 HOH HOH . J 5 HOH B 1 501 90 HOH HOH . J 5 HOH B 2 502 21 HOH HOH . J 5 HOH B 3 503 92 HOH HOH . J 5 HOH B 4 504 50 HOH HOH . J 5 HOH B 5 505 23 HOH HOH . J 5 HOH B 6 506 56 HOH HOH . J 5 HOH B 7 507 51 HOH HOH . J 5 HOH B 8 508 55 HOH HOH . J 5 HOH B 9 509 22 HOH HOH . J 5 HOH B 10 510 58 HOH HOH . J 5 HOH B 11 511 17 HOH HOH . J 5 HOH B 12 512 34 HOH HOH . J 5 HOH B 13 513 63 HOH HOH . J 5 HOH B 14 514 28 HOH HOH . J 5 HOH B 15 515 40 HOH HOH . J 5 HOH B 16 516 18 HOH HOH . J 5 HOH B 17 517 57 HOH HOH . J 5 HOH B 18 518 2 HOH HOH . J 5 HOH B 19 519 79 HOH HOH . J 5 HOH B 20 520 8 HOH HOH . J 5 HOH B 21 521 6 HOH HOH . J 5 HOH B 22 522 80 HOH HOH . J 5 HOH B 23 523 12 HOH HOH . J 5 HOH B 24 524 14 HOH HOH . J 5 HOH B 25 525 16 HOH HOH . J 5 HOH B 26 526 54 HOH HOH . J 5 HOH B 27 527 82 HOH HOH . J 5 HOH B 28 528 70 HOH HOH . J 5 HOH B 29 529 38 HOH HOH . J 5 HOH B 30 530 44 HOH HOH . J 5 HOH B 31 531 43 HOH HOH . J 5 HOH B 32 532 60 HOH HOH . J 5 HOH B 33 533 39 HOH HOH . J 5 HOH B 34 534 19 HOH HOH . J 5 HOH B 35 535 27 HOH HOH . J 5 HOH B 36 536 88 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 -26.207 36.434 -18.026 1 53.9 ? O4 DST 401 A 1 HETATM 2 P P1 DST . . . C 2 -24.7 36.608 -18.109 1 54.1 ? P1 DST 401 A 1 HETATM 3 O O6 DST . . . C 2 -24.309 38.033 -18.459 1 55.18 ? O6 DST 401 A 1 HETATM 4 O O5 DST . . . C 2 -24.137 35.672 -19.162 1 47.26 ? O5 DST 401 A 1 HETATM 5 O O2 DST . . . C 2 -24.049 36.182 -16.671 1 50.42 ? O2 DST 401 A 1 HETATM 6 P P3 DST . . . C 2 -22.458 35.813 -16.459 1 41.09 ? P3 DST 401 A 1 HETATM 7 O O8 DST . . . C 2 -21.714 35.954 -17.77 1 58.28 ? O8 DST 401 A 1 HETATM 8 O O7 DST . . . C 2 -21.801 36.75 -15.476 1 56.2 ? O7 DST 401 A 1 HETATM 9 S S9 DST . . . C 2 -22.332 33.815 -15.863 1 67.54 ? S9 DST 401 A 1 HETATM 10 C C10 DST . . . C 2 -20.675 33.253 -16.357 1 76.34 ? C10 DST 401 A 1 HETATM 11 C C11 DST . . . C 2 -19.683 34.224 -15.735 1 79.4 ? C11 DST 401 A 1 HETATM 12 C C12 DST . . . C 2 -19.083 33.883 -14.612 1 74.75 ? C12 DST 401 A 1 HETATM 13 C C13 DST . . . C 2 -18.081 34.822 -13.959 1 79.4 ? C13 DST 401 A 1 HETATM 14 C C14 DST . . . C 2 -19.39 32.531 -13.978 1 78.71 ? C14 DST 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #