data_5Z45 # _model_server_result.job_id JXiBjc8C0LAEoB5QdqV2Zw _model_server_result.datetime_utc '2024-11-25 02:36:23' _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 5z45 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5Z45 # _exptl.entry_id 5Z45 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 330.275 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL 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 _cell.angle_gamma 90 _cell.entry_id 5Z45 _cell.length_a 116.257 _cell.length_b 116.257 _cell.length_c 49.687 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z45 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H 1 1 B,E,F,G,I 2 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 E 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 covale ? covale1 A NZ LYS 278 A LYS 278 1_555 C O2A GST . A GST 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? metalc ? metalc1 A OD1 ASN 41 A ASN 41 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc2 A OE2 GLU 63 A GLU 63 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc3 A OD2 ASP 65 A ASP 65 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? metalc ? metalc4 B OD1 ASN 41 B ASN 41 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc5 B OE1 GLU 63 B GLU 63 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? # _chem_comp.formula 'C10 H20 O6 P2 S' _chem_comp.formula_weight 330.275 _chem_comp.id GST _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL S-THIOLODIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE' # 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 PA O1A GST sing 151 n n PA O2A GST doub 152 n n PA O3A GST sing 153 n n PA O1B GST sing 154 n n O1A H1A GST sing 155 n n O3A H3A GST sing 156 n n O1B PB GST sing 157 n n PB O2B GST doub 158 n n PB O3B GST sing 159 n n PB S1 GST sing 160 n n O3B H3B GST sing 161 n n S1 C1 GST sing 162 n n C1 C2 GST sing 163 n n C1 H11 GST sing 164 n n C1 H12 GST sing 165 n n C2 C3 GST doub 166 e n C2 H2 GST sing 167 n n C3 C10 GST sing 168 n n C3 C4 GST sing 169 n n C10 H101 GST sing 170 n n C10 H102 GST sing 171 n n C10 H103 GST sing 172 n n C4 C5 GST sing 173 n n C4 H41 GST sing 174 n n C4 H42 GST sing 175 n n C5 C6 GST sing 176 n n C5 H51 GST sing 177 n n C5 H52 GST sing 178 n n C6 C7 GST doub 179 n n C6 H6 GST sing 180 n n C7 C9 GST sing 181 n n C7 C8 GST sing 182 n n C9 H91 GST sing 183 n n C9 H92 GST sing 184 n n C9 H93 GST sing 185 n n C8 H81 GST sing 186 n n C8 H82 GST sing 187 n n C8 H83 GST sing 188 n n # _atom_sites.entry_id 5Z45 _atom_sites.fract_transf_matrix[1][1] 0.008602 _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] 0.008602 _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] 0.020126 _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 GST A 1 401 2 GST GST . D 3 MG A 1 402 2 MG MG . E 2 GST B 1 401 1 GST GST . F 4 8XL B 1 402 1 8XL LIG . G 3 MG B 1 403 1 MG MG . H 5 HOH A 1 501 2 HOH HOH . H 5 HOH A 2 502 17 HOH HOH . H 5 HOH A 3 503 16 HOH HOH . H 5 HOH A 4 504 8 HOH HOH . H 5 HOH A 5 505 9 HOH HOH . H 5 HOH A 6 506 19 HOH HOH . H 5 HOH A 7 507 6 HOH HOH . H 5 HOH A 8 508 25 HOH HOH . H 5 HOH A 9 509 13 HOH HOH . H 5 HOH A 10 510 21 HOH HOH . H 5 HOH A 11 511 24 HOH HOH . I 5 HOH B 1 501 20 HOH HOH . I 5 HOH B 2 502 7 HOH HOH . I 5 HOH B 3 503 18 HOH HOH . I 5 HOH B 4 504 26 HOH HOH . I 5 HOH B 5 505 10 HOH HOH . I 5 HOH B 6 506 5 HOH HOH . I 5 HOH B 7 507 4 HOH HOH . I 5 HOH B 8 508 3 HOH HOH . I 5 HOH B 9 509 15 HOH HOH . I 5 HOH B 10 510 23 HOH HOH . I 5 HOH B 11 511 14 HOH HOH . I 5 HOH B 12 512 1 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 P PA GST . . . E 2 29.98 181.59 -22.876 0.84 68.71 ? PA GST 401 B 1 HETATM 2 O O1A GST . . . E 2 31.412 181.157 -22.97 0.84 64.09 ? O1A GST 401 B 1 HETATM 3 O O2A GST . . . E 2 29.409 181.756 -24.267 0.84 78.82 ? O2A GST 401 B 1 HETATM 4 O O3A GST . . . E 2 29.697 182.762 -21.963 0.84 63.56 ? O3A GST 401 B 1 HETATM 5 O O1B GST . . . E 2 29.153 180.3 -22.352 0.84 67.89 ? O1B GST 401 B 1 HETATM 6 P PB GST . . . E 2 29.588 178.909 -21.678 0.84 52.52 ? PB GST 401 B 1 HETATM 7 O O2B GST . . . E 2 30.792 178.451 -22.376 0.84 52.75 ? O2B GST 401 B 1 HETATM 8 O O3B GST . . . E 2 29.84 179.084 -20.102 0.84 60.24 ? O3B GST 401 B 1 HETATM 9 S S1 GST . . . E 2 28.183 177.508 -22.073 0.84 50.74 ? S1 GST 401 B 1 HETATM 10 C C1 GST . . . E 2 28.713 175.99 -21.32 0.84 53.65 ? C1 GST 401 B 1 HETATM 11 C C2 GST . . . E 2 28.302 175.924 -19.866 0.84 55.23 ? C2 GST 401 B 1 HETATM 12 C C3 GST . . . E 2 27.341 175.117 -19.386 0.84 53.15 ? C3 GST 401 B 1 HETATM 13 C C10 GST . . . E 2 27.056 175.124 -17.921 0.84 44.59 ? C10 GST 401 B 1 HETATM 14 C C4 GST . . . E 2 26.526 174.206 -20.277 0.84 65.22 ? C4 GST 401 B 1 HETATM 15 C C5 GST . . . E 2 25.582 173.317 -19.451 0.84 68.43 ? C5 GST 401 B 1 HETATM 16 C C6 GST . . . E 2 25.687 171.846 -19.848 0.84 72.14 ? C6 GST 401 B 1 HETATM 17 C C7 GST . . . E 2 26.544 170.982 -19.259 0.84 77.69 ? C7 GST 401 B 1 HETATM 18 C C9 GST . . . E 2 27.477 171.453 -18.183 0.84 73.1 ? C9 GST 401 B 1 HETATM 19 C C8 GST . . . E 2 26.576 169.545 -19.699 0.84 80.35 ? C8 GST 401 B 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #