data_4OD5 # _model_server_result.job_id oeKmJsNdkvtySU50KH4G4A _model_server_result.datetime_utc '2024-11-05 01:01:46' _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 4od5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 4OD5 # _exptl.entry_id 4OD5 _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 6 _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 4OD5 _cell.length_a 70.104 _cell.length_b 122.829 _cell.length_c 423.416 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4OD5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,H,I,J,EA 1 1 B,K,L,M,N,FA 2 1 C,O,P,Q,R,GA 3 1 D,S,T,U,V,HA 4 1 E,W,X,Y,Z,IA 5 1 F,AA,BA,CA,DA,JA 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 ? 2 G N N ? 2 K N N ? 2 O N N ? 2 S N N ? 2 W N N ? 2 AA 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 metalc ? metalc1 A OD1 ASP 77 A ASP 58 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 G O1A GST . A GST 301 1_555 I MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc3 G O3A GST . A GST 301 1_555 J MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc4 J MG MG . A MG 304 1_555 EA O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc5 B OD1 ASP 77 B ASP 58 1_555 M MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc6 K O1A GST . B GST 301 1_555 M MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc7 K O3A GST . B GST 301 1_555 N MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc8 K O3B GST . B GST 301 1_555 N MG MG . B MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc9 N MG MG . B MG 304 1_555 FA O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc10 C OD1 ASP 77 C ASP 58 1_555 Q MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc11 O O1A GST . C GST 301 1_555 Q MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc12 O O3A GST . C GST 301 1_555 R MG MG . C MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc13 O O3B GST . C GST 301 1_555 R MG MG . C MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc14 R MG MG . C MG 304 1_555 GA O HOH . C HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc15 D OD1 ASP 77 D ASP 58 1_555 U MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc16 S O1A GST . D GST 301 1_555 U MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc17 S O3A GST . D GST 301 1_555 V MG MG . D MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc18 V MG MG . D MG 304 1_555 HA O HOH . D HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc19 E OD1 ASP 77 E ASP 58 1_555 Y MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc20 W O1A GST . E GST 301 1_555 Y MG MG . E MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc21 W O3A GST . E GST 301 1_555 Z MG MG . E MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc22 Z MG MG . E MG 304 1_555 IA O HOH . E HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc23 F OD1 ASP 77 F ASP 58 1_555 CA MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc24 AA O1A GST . F GST 301 1_555 CA MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc25 AA O3A GST . F GST 301 1_555 DA MG MG . F MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc26 AA O3B GST . F GST 301 1_555 DA MG MG . F MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc27 DA MG MG . F MG 304 1_555 JA O HOH . F HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? # _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 116 n n PA O2A GST doub 117 n n PA O3A GST sing 118 n n PA O1B GST sing 119 n n O1A H1A GST sing 120 n n O3A H3A GST sing 121 n n O1B PB GST sing 122 n n PB O2B GST doub 123 n n PB O3B GST sing 124 n n PB S1 GST sing 125 n n O3B H3B GST sing 126 n n S1 C1 GST sing 127 n n C1 C2 GST sing 128 n n C1 H11 GST sing 129 n n C1 H12 GST sing 130 n n C2 C3 GST doub 131 e n C2 H2 GST sing 132 n n C3 C10 GST sing 133 n n C3 C4 GST sing 134 n n C10 H101 GST sing 135 n n C10 H102 GST sing 136 n n C10 H103 GST sing 137 n n C4 C5 GST sing 138 n n C4 H41 GST sing 139 n n C4 H42 GST sing 140 n n C5 C6 GST sing 141 n n C5 H51 GST sing 142 n n C5 H52 GST sing 143 n n C6 C7 GST doub 144 n n C6 H6 GST sing 145 n n C7 C9 GST sing 146 n n C7 C8 GST sing 147 n n C9 H91 GST sing 148 n n C9 H92 GST sing 149 n n C9 H93 GST sing 150 n n C8 H81 GST sing 151 n n C8 H82 GST sing 152 n n C8 H83 GST sing 153 n n # _atom_sites.entry_id 4OD5 _atom_sites.fract_transf_matrix[1][1] 0.014265 _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] 0.008141 _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] 0.002362 _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 G 2 GST A 1 301 395 GST GST . H 3 PHB A 1 302 396 PHB PHB . I 4 MG A 1 303 398 MG MG . J 4 MG A 1 304 400 MG MG . K 2 GST B 1 301 395 GST GST . L 3 PHB B 1 302 396 PHB PHB . M 4 MG B 1 303 398 MG MG . N 4 MG B 1 304 400 MG MG . O 2 GST C 1 301 395 GST GST . P 3 PHB C 1 302 396 PHB PHB . Q 4 MG C 1 303 398 MG MG . R 4 MG C 1 304 400 MG MG . S 2 GST D 1 301 395 GST GST . T 3 PHB D 1 302 396 PHB PHB . U 4 MG D 1 303 398 MG MG . V 4 MG D 1 304 400 MG MG . W 2 GST E 1 301 395 GST GST . X 3 PHB E 1 302 396 PHB PHB . Y 4 MG E 1 303 398 MG MG . Z 4 MG E 1 304 400 MG MG . AA 2 GST F 1 301 395 GST GST . BA 3 PHB F 1 302 396 PHB PHB . CA 4 MG F 1 303 398 MG MG . DA 4 MG F 1 304 400 MG MG . EA 5 HOH A 1 401 397 HOH HOH . FA 5 HOH B 1 401 397 HOH HOH . GA 5 HOH C 1 401 397 HOH HOH . HA 5 HOH D 1 401 397 HOH HOH . IA 5 HOH E 1 401 397 HOH HOH . JA 5 HOH F 1 401 397 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 . . . G 2 65.97 13.871 101.184 1 153.96 ? PA GST 301 A 1 HETATM 2 O O1A GST . . . G 2 64.494 13.688 100.864 1 152.73 ? O1A GST 301 A 1 HETATM 3 O O2A GST . . . G 2 66.21 15.276 101.685 1 146.18 ? O2A GST 301 A 1 HETATM 4 O O3A GST . . . G 2 66.356 12.89 102.267 1 140.05 ? O3A GST 301 A 1 HETATM 5 O O1B GST . . . G 2 66.885 13.606 99.911 1 140.39 ? O1B GST 301 A 1 HETATM 6 P PB GST . . . G 2 68.476 13.59 99.914 1 120.02 ? PB GST 301 A 1 HETATM 7 O O2B GST . . . G 2 68.966 12.525 98.959 1 116.53 ? O2B GST 301 A 1 HETATM 8 O O3B GST . . . G 2 68.981 13.274 101.303 1 107.8 ? O3B GST 301 A 1 HETATM 9 S S1 GST . . . G 2 69.27 15.41 99.322 1 90.19 ? S1 GST 301 A 1 HETATM 10 C C1 GST . . . G 2 70.978 15.494 99.808 1 70.65 ? C1 GST 301 A 1 HETATM 11 C C2 GST . . . G 2 71.876 15.744 98.61 1 59.01 ? C2 GST 301 A 1 HETATM 12 C C3 GST . . . G 2 72.503 16.93 98.448 1 53.76 ? C3 GST 301 A 1 HETATM 13 C C10 GST . . . G 2 72.086 18.136 99.261 1 52.52 ? C10 GST 301 A 1 HETATM 14 C C4 GST . . . G 2 73.562 17.077 97.377 1 48.02 ? C4 GST 301 A 1 HETATM 15 C C5 GST . . . G 2 74.354 15.792 97.264 1 42.69 ? C5 GST 301 A 1 HETATM 16 C C6 GST . . . G 2 75.359 15.939 96.146 1 35.03 ? C6 GST 301 A 1 HETATM 17 C C7 GST . . . G 2 75.061 15.442 94.932 1 30.65 ? C7 GST 301 A 1 HETATM 18 C C9 GST . . . G 2 74.628 13.996 94.809 1 31.74 ? C9 GST 301 A 1 HETATM 19 C C8 GST . . . G 2 74.818 16.397 93.781 1 28.53 ? C8 GST 301 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 19 #