data_5KCY # _model_server_result.job_id jkJy-1OOFfQ2-g5x2M8rlw _model_server_result.datetime_utc '2024-11-05 03:56:14' _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 5kcy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 5KCY # _exptl.entry_id 5KCY _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 5KCY _cell.length_a 96.95 _cell.length_b 134.91 _cell.length_c 68.69 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KCY _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 1 193.9 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 F N N # _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 5KCY _atom_sites.fract_transf_matrix[1][1] 0.010315 _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] 0.007412 _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] 0.014558 _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 1 XBU DBU . D 3 GST A 1 502 3 GST GPP . E 2 XBU B 1 501 2 XBU DBU . F 3 GST B 1 502 4 GST GPP . G 4 HOH A 1 601 151 HOH HOH . G 4 HOH A 2 602 7 HOH HOH . G 4 HOH A 3 603 22 HOH HOH . G 4 HOH A 4 604 68 HOH HOH . G 4 HOH A 5 605 61 HOH HOH . G 4 HOH A 6 606 30 HOH HOH . G 4 HOH A 7 607 6 HOH HOH . G 4 HOH A 8 608 9 HOH HOH . G 4 HOH A 9 609 101 HOH HOH . G 4 HOH A 10 610 106 HOH HOH . G 4 HOH A 11 611 26 HOH HOH . G 4 HOH A 12 612 3 HOH HOH . G 4 HOH A 13 613 121 HOH HOH . G 4 HOH A 14 614 49 HOH HOH . G 4 HOH A 15 615 21 HOH HOH . G 4 HOH A 16 616 70 HOH HOH . G 4 HOH A 17 617 56 HOH HOH . G 4 HOH A 18 618 27 HOH HOH . G 4 HOH A 19 619 127 HOH HOH . G 4 HOH A 20 620 14 HOH HOH . G 4 HOH A 21 621 66 HOH HOH . G 4 HOH A 22 622 103 HOH HOH . G 4 HOH A 23 623 12 HOH HOH . G 4 HOH A 24 624 99 HOH HOH . G 4 HOH A 25 625 20 HOH HOH . G 4 HOH A 26 626 40 HOH HOH . G 4 HOH A 27 627 107 HOH HOH . G 4 HOH A 28 628 24 HOH HOH . G 4 HOH A 29 629 33 HOH HOH . G 4 HOH A 30 630 52 HOH HOH . G 4 HOH A 31 631 81 HOH HOH . G 4 HOH A 32 632 19 HOH HOH . G 4 HOH A 33 633 84 HOH HOH . G 4 HOH A 34 634 60 HOH HOH . G 4 HOH A 35 635 46 HOH HOH . G 4 HOH A 36 636 102 HOH HOH . H 4 HOH B 1 601 33 HOH HOH . H 4 HOH B 2 602 11 HOH HOH . H 4 HOH B 3 603 24 HOH HOH . H 4 HOH B 4 604 37 HOH HOH . H 4 HOH B 5 605 36 HOH HOH . H 4 HOH B 6 606 13 HOH HOH . H 4 HOH B 7 607 18 HOH HOH . H 4 HOH B 8 608 76 HOH HOH . H 4 HOH B 9 609 25 HOH HOH . H 4 HOH B 10 610 65 HOH HOH . H 4 HOH B 11 611 42 HOH HOH . H 4 HOH B 12 612 158 HOH HOH . H 4 HOH B 13 613 47 HOH HOH . H 4 HOH B 14 614 39 HOH HOH . H 4 HOH B 15 615 85 HOH HOH . H 4 HOH B 16 616 72 HOH HOH . H 4 HOH B 17 617 15 HOH HOH . H 4 HOH B 18 618 90 HOH HOH . H 4 HOH B 19 619 54 HOH HOH . H 4 HOH B 20 620 31 HOH HOH . H 4 HOH B 21 621 36 HOH HOH . H 4 HOH B 22 622 68 HOH HOH . H 4 HOH B 23 623 31 HOH HOH . H 4 HOH B 24 624 32 HOH HOH . H 4 HOH B 25 625 1 HOH HOH . H 4 HOH B 26 626 8 HOH HOH . H 4 HOH B 27 627 110 HOH HOH . H 4 HOH B 28 628 64 HOH HOH . H 4 HOH B 29 629 88 HOH HOH . H 4 HOH B 30 630 105 HOH HOH . H 4 HOH B 31 631 91 HOH HOH . H 4 HOH B 32 632 147 HOH HOH . H 4 HOH B 33 633 51 HOH HOH . H 4 HOH B 34 634 72 HOH HOH . H 4 HOH B 35 635 51 HOH HOH . H 4 HOH B 36 636 45 HOH HOH . H 4 HOH B 37 637 98 HOH HOH . H 4 HOH B 38 638 28 HOH HOH . H 4 HOH B 39 639 161 HOH HOH . H 4 HOH B 40 640 85 HOH HOH . H 4 HOH B 41 641 46 HOH HOH . H 4 HOH B 42 642 63 HOH HOH . H 4 HOH B 43 643 4 HOH HOH . H 4 HOH B 44 644 116 HOH HOH . H 4 HOH B 45 645 79 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 . . . F 3 73.288 14.653 26.433 1 43.86 ? PA GST 502 B 1 HETATM 2 O O1A GST . . . F 3 72.269 15.418 27.338 1 52.06 ? O1A GST 502 B 1 HETATM 3 O O2A GST . . . F 3 72.888 14.502 24.891 1 45.18 ? O2A GST 502 B 1 HETATM 4 O O3A GST . . . F 3 74.615 15.425 26.43 1 46.63 ? O3A GST 502 B 1 HETATM 5 O O1B GST . . . F 3 72.791 13.227 27.017 1 46.94 ? O1B GST 502 B 1 HETATM 6 P PB GST . . . F 3 72.95 12.596 28.554 1 47.54 ? PB GST 502 B 1 HETATM 7 O O2B GST . . . F 3 73.61 11.142 28.323 1 38.11 ? O2B GST 502 B 1 HETATM 8 O O3B GST . . . F 3 73.817 13.457 29.414 1 49.83 ? O3B GST 502 B 1 HETATM 9 S S1 GST . . . F 3 71.044 12.236 29.367 1 44.03 ? S1 GST 502 B 1 HETATM 10 C C1 GST . . . F 3 71.373 11.049 30.78 1 50.54 ? C1 GST 502 B 1 HETATM 11 C C2 GST . . . F 3 69.886 10.818 31.109 1 50.9 ? C2 GST 502 B 1 HETATM 12 C C3 GST . . . F 3 69.05 9.6 30.71 1 47.81 ? C3 GST 502 B 1 HETATM 13 C C10 GST . . . F 3 69.581 8.351 30.064 1 53.71 ? C10 GST 502 B 1 HETATM 14 C C4 GST . . . F 3 67.578 9.697 30.85 1 51.62 ? C4 GST 502 B 1 HETATM 15 C C5 GST . . . F 3 67.247 9.567 32.256 1 49.59 ? C5 GST 502 B 1 HETATM 16 C C6 GST . . . F 3 66.56 10.831 32.728 1 46.65 ? C6 GST 502 B 1 HETATM 17 C C7 GST . . . F 3 65.182 10.84 33.383 1 41.34 ? C7 GST 502 B 1 HETATM 18 C C9 GST . . . F 3 64.195 9.687 33.439 1 35.73 ? C9 GST 502 B 1 HETATM 19 C C8 GST . . . F 3 64.789 12.153 33.96 1 47.95 ? C8 GST 502 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 19 #