data_5KD0 # _model_server_result.job_id sFSUlzN0pm2Q-m3hhdlnhg _model_server_result.datetime_utc '2024-11-24 01:19:07' _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 5kd0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 5KD0 # _exptl.entry_id 5KD0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 330.275 _entity.id 3 _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 5KD0 _cell.length_a 96.69 _cell.length_b 139.24 _cell.length_c 68.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KD0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 193.38 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id O _struct_conn.ptnr1_label_comp_id TRP _struct_conn.ptnr1_label_seq_id 25 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id TRP _struct_conn.ptnr1_auth_seq_id 30 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id CG2 _struct_conn.ptnr2_label_comp_id THR _struct_conn.ptnr2_label_seq_id 29 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id THR _struct_conn.ptnr2_auth_seq_id 34 _struct_conn.ptnr2_symmetry 1_555 _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 1.181 _struct_conn.pdbx_value_order ? # _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 129 n n PA O2A GST doub 130 n n PA O3A GST sing 131 n n PA O1B GST sing 132 n n O1A H1A GST sing 133 n n O3A H3A GST sing 134 n n O1B PB GST sing 135 n n PB O2B GST doub 136 n n PB O3B GST sing 137 n n PB S1 GST sing 138 n n O3B H3B GST sing 139 n n S1 C1 GST sing 140 n n C1 C2 GST sing 141 n n C1 H11 GST sing 142 n n C1 H12 GST sing 143 n n C2 C3 GST doub 144 e n C2 H2 GST sing 145 n n C3 C10 GST sing 146 n n C3 C4 GST sing 147 n n C10 H101 GST sing 148 n n C10 H102 GST sing 149 n n C10 H103 GST sing 150 n n C4 C5 GST sing 151 n n C4 H41 GST sing 152 n n C4 H42 GST sing 153 n n C5 C6 GST sing 154 n n C5 H51 GST sing 155 n n C5 H52 GST sing 156 n n C6 C7 GST doub 157 n n C6 H6 GST sing 158 n n C7 C9 GST sing 159 n n C7 C8 GST sing 160 n n C9 H91 GST sing 161 n n C9 H92 GST sing 162 n n C9 H93 GST sing 163 n n C8 H81 GST sing 164 n n C8 H82 GST sing 165 n n C8 H83 GST sing 166 n n # _atom_sites.entry_id 5KD0 _atom_sites.fract_transf_matrix[1][1] 0.010342 _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] 0.007182 _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] 0.014535 _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 XBU A 1 501 2 XBU DBU . D 3 GST A 1 502 1 GST GPP . E 3 GST B 1 501 1 GST GPP . F 4 HOH A 1 601 33 HOH HOH . F 4 HOH A 2 602 32 HOH HOH . F 4 HOH A 3 603 17 HOH HOH . F 4 HOH A 4 604 3 HOH HOH . G 4 HOH B 1 601 29 HOH HOH . G 4 HOH B 2 602 18 HOH HOH . G 4 HOH B 3 603 9 HOH HOH . G 4 HOH B 4 604 13 HOH HOH . G 4 HOH B 5 605 16 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 3 74.451 16.288 26.005 1 60.01 ? PA GST 501 B 1 HETATM 2 O O1A GST . . . E 3 74.242 17.363 27.194 1 60.34 ? O1A GST 501 B 1 HETATM 3 O O2A GST . . . E 3 73.344 16.502 24.859 1 67.25 ? O2A GST 501 B 1 HETATM 4 O O3A GST . . . E 3 75.78 16.481 25.378 1 59.7 ? O3A GST 501 B 1 HETATM 5 O O1B GST . . . E 3 74.035 14.84 26.53 1 66.16 ? O1B GST 501 B 1 HETATM 6 P PB GST . . . E 3 73.713 14.509 28.095 1 81.64 ? PB GST 501 B 1 HETATM 7 O O2B GST . . . E 3 74.712 13.26 28.503 1 75.65 ? O2B GST 501 B 1 HETATM 8 O O3B GST . . . E 3 73.886 15.677 29.011 1 75.51 ? O3B GST 501 B 1 HETATM 9 S S1 GST . . . E 3 72.197 13.795 28.135 1 79.83 ? S1 GST 501 B 1 HETATM 10 C C1 GST . . . E 3 72.016 13.616 29.927 1 75.52 ? C1 GST 501 B 1 HETATM 11 C C2 GST . . . E 3 70.654 12.908 30.08 1 74.66 ? C2 GST 501 B 1 HETATM 12 C C3 GST . . . E 3 70.096 12.382 31.412 1 69.05 ? C3 GST 501 B 1 HETATM 13 C C10 GST . . . E 3 70.886 12.495 32.713 1 67.2 ? C10 GST 501 B 1 HETATM 14 C C4 GST . . . E 3 68.748 11.714 31.409 1 67.44 ? C4 GST 501 B 1 HETATM 15 C C5 GST . . . E 3 67.783 12.622 32.159 1 64.25 ? C5 GST 501 B 1 HETATM 16 C C6 GST . . . E 3 66.55 11.73 32.371 1 60.11 ? C6 GST 501 B 1 HETATM 17 C C7 GST . . . E 3 65.546 11.97 33.501 1 59.88 ? C7 GST 501 B 1 HETATM 18 C C9 GST . . . E 3 65.663 13.142 34.484 1 58.11 ? C9 GST 501 B 1 HETATM 19 C C8 GST . . . E 3 64.386 10.993 33.65 1 59.33 ? C8 GST 501 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 436 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 19 #