data_5KCL # _model_server_result.job_id '_GUZiKoGMbItF91iLF49AQ' _model_server_result.datetime_utc '2024-11-24 04:21:41' _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 5kcl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5KCL # _exptl.entry_id 5KCL _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 _cell.angle_gamma 90 _cell.entry_id 5KCL _cell.length_a 96.29 _cell.length_b 132.97 _cell.length_c 68.48 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KCL _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 _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 1 192.58 0 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 D N N # _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 5KCL _atom_sites.fract_transf_matrix[1][1] 0.010385 _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] 0.00752 _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] 0.014603 _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 1 501 1 DST DRG . D 2 DST B 1 501 2 DST DRG . E 3 HOH A 1 601 106 HOH HOH . E 3 HOH A 2 602 27 HOH HOH . E 3 HOH A 3 603 19 HOH HOH . E 3 HOH A 4 604 9 HOH HOH . E 3 HOH A 5 605 124 HOH HOH . E 3 HOH A 6 606 38 HOH HOH . E 3 HOH A 7 607 62 HOH HOH . E 3 HOH A 8 608 76 HOH HOH . E 3 HOH A 9 609 104 HOH HOH . E 3 HOH A 10 610 31 HOH HOH . E 3 HOH A 11 611 101 HOH HOH . E 3 HOH A 12 612 102 HOH HOH . E 3 HOH A 13 613 44 HOH HOH . E 3 HOH A 14 614 35 HOH HOH . E 3 HOH A 15 615 24 HOH HOH . E 3 HOH A 16 616 42 HOH HOH . E 3 HOH A 17 617 67 HOH HOH . E 3 HOH A 18 618 61 HOH HOH . E 3 HOH A 19 619 163 HOH HOH . E 3 HOH A 20 620 32 HOH HOH . E 3 HOH A 21 621 120 HOH HOH . E 3 HOH A 22 622 31 HOH HOH . E 3 HOH A 23 623 172 HOH HOH . E 3 HOH A 24 624 8 HOH HOH . E 3 HOH A 25 625 48 HOH HOH . E 3 HOH A 26 626 38 HOH HOH . E 3 HOH A 27 627 10 HOH HOH . E 3 HOH A 28 628 99 HOH HOH . E 3 HOH A 29 629 68 HOH HOH . E 3 HOH A 30 630 17 HOH HOH . E 3 HOH A 31 631 41 HOH HOH . E 3 HOH A 32 632 147 HOH HOH . E 3 HOH A 33 633 34 HOH HOH . E 3 HOH A 34 634 39 HOH HOH . E 3 HOH A 35 635 105 HOH HOH . E 3 HOH A 36 636 195 HOH HOH . E 3 HOH A 37 637 36 HOH HOH . E 3 HOH A 38 638 40 HOH HOH . E 3 HOH A 39 639 139 HOH HOH . E 3 HOH A 40 640 130 HOH HOH . E 3 HOH A 41 641 60 HOH HOH . E 3 HOH A 42 642 91 HOH HOH . E 3 HOH A 43 643 57 HOH HOH . E 3 HOH A 44 644 37 HOH HOH . E 3 HOH A 45 645 30 HOH HOH . E 3 HOH A 46 646 6 HOH HOH . E 3 HOH A 47 647 51 HOH HOH . E 3 HOH A 48 648 118 HOH HOH . E 3 HOH A 49 649 26 HOH HOH . E 3 HOH A 50 650 113 HOH HOH . E 3 HOH A 51 651 209 HOH HOH . E 3 HOH A 52 652 5 HOH HOH . E 3 HOH A 53 653 123 HOH HOH . E 3 HOH A 54 654 54 HOH HOH . E 3 HOH A 55 655 20 HOH HOH . E 3 HOH A 56 656 33 HOH HOH . E 3 HOH A 57 657 29 HOH HOH . E 3 HOH A 58 658 133 HOH HOH . E 3 HOH A 59 659 230 HOH HOH . E 3 HOH A 60 660 73 HOH HOH . E 3 HOH A 61 661 51 HOH HOH . E 3 HOH A 62 662 41 HOH HOH . E 3 HOH A 63 663 95 HOH HOH . E 3 HOH A 64 664 39 HOH HOH . E 3 HOH A 65 665 146 HOH HOH . E 3 HOH A 66 666 52 HOH HOH . E 3 HOH A 67 667 35 HOH HOH . E 3 HOH A 68 668 22 HOH HOH . E 3 HOH A 69 669 70 HOH HOH . E 3 HOH A 70 670 55 HOH HOH . E 3 HOH A 71 671 71 HOH HOH . E 3 HOH A 72 672 29 HOH HOH . E 3 HOH A 73 673 142 HOH HOH . E 3 HOH A 74 674 65 HOH HOH . E 3 HOH A 75 675 43 HOH HOH . E 3 HOH A 76 676 220 HOH HOH . E 3 HOH A 77 677 80 HOH HOH . E 3 HOH A 78 678 51 HOH HOH . E 3 HOH A 79 679 60 HOH HOH . E 3 HOH A 80 680 47 HOH HOH . E 3 HOH A 81 681 100 HOH HOH . E 3 HOH A 82 682 18 HOH HOH . E 3 HOH A 83 683 250 HOH HOH . E 3 HOH A 84 684 233 HOH HOH . E 3 HOH A 85 685 82 HOH HOH . E 3 HOH A 86 686 248 HOH HOH . E 3 HOH A 87 687 36 HOH HOH . E 3 HOH A 88 688 193 HOH HOH . E 3 HOH A 89 689 189 HOH HOH . E 3 HOH A 90 690 161 HOH HOH . E 3 HOH A 91 691 92 HOH HOH . E 3 HOH A 92 692 246 HOH HOH . E 3 HOH A 93 693 132 HOH HOH . E 3 HOH A 94 694 81 HOH HOH . E 3 HOH A 95 695 138 HOH HOH . E 3 HOH A 96 696 256 HOH HOH . E 3 HOH A 97 697 167 HOH HOH . E 3 HOH A 98 698 130 HOH HOH . F 3 HOH B 1 601 180 HOH HOH . F 3 HOH B 2 602 22 HOH HOH . F 3 HOH B 3 603 194 HOH HOH . F 3 HOH B 4 604 93 HOH HOH . F 3 HOH B 5 605 26 HOH HOH . F 3 HOH B 6 606 12 HOH HOH . F 3 HOH B 7 607 16 HOH HOH . F 3 HOH B 8 608 22 HOH HOH . F 3 HOH B 9 609 84 HOH HOH . F 3 HOH B 10 610 185 HOH HOH . F 3 HOH B 11 611 39 HOH HOH . F 3 HOH B 12 612 54 HOH HOH . F 3 HOH B 13 613 57 HOH HOH . F 3 HOH B 14 614 7 HOH HOH . F 3 HOH B 15 615 13 HOH HOH . F 3 HOH B 16 616 23 HOH HOH . F 3 HOH B 17 617 38 HOH HOH . F 3 HOH B 18 618 56 HOH HOH . F 3 HOH B 19 619 63 HOH HOH . F 3 HOH B 20 620 49 HOH HOH . F 3 HOH B 21 621 257 HOH HOH . F 3 HOH B 22 622 113 HOH HOH . F 3 HOH B 23 623 27 HOH HOH . F 3 HOH B 24 624 95 HOH HOH . F 3 HOH B 25 625 63 HOH HOH . F 3 HOH B 26 626 217 HOH HOH . F 3 HOH B 27 627 25 HOH HOH . F 3 HOH B 28 628 46 HOH HOH . F 3 HOH B 29 629 170 HOH HOH . F 3 HOH B 30 630 94 HOH HOH . F 3 HOH B 31 631 94 HOH HOH . F 3 HOH B 32 632 62 HOH HOH . F 3 HOH B 33 633 24 HOH HOH . F 3 HOH B 34 634 121 HOH HOH . F 3 HOH B 35 635 3 HOH HOH . F 3 HOH B 36 636 25 HOH HOH . F 3 HOH B 37 637 1 HOH HOH . F 3 HOH B 38 638 74 HOH HOH . F 3 HOH B 39 639 48 HOH HOH . F 3 HOH B 40 640 75 HOH HOH . F 3 HOH B 41 641 14 HOH HOH . F 3 HOH B 42 642 107 HOH HOH . F 3 HOH B 43 643 90 HOH HOH . F 3 HOH B 44 644 52 HOH HOH . F 3 HOH B 45 645 4 HOH HOH . F 3 HOH B 46 646 62 HOH HOH . F 3 HOH B 47 647 184 HOH HOH . F 3 HOH B 48 648 201 HOH HOH . F 3 HOH B 49 649 131 HOH HOH . F 3 HOH B 50 650 1 HOH HOH . F 3 HOH B 51 651 31 HOH HOH . F 3 HOH B 52 652 204 HOH HOH . F 3 HOH B 53 653 187 HOH HOH . F 3 HOH B 54 654 132 HOH HOH . F 3 HOH B 55 655 58 HOH HOH . F 3 HOH B 56 656 140 HOH HOH . F 3 HOH B 57 657 143 HOH HOH . F 3 HOH B 58 658 43 HOH HOH . F 3 HOH B 59 659 179 HOH HOH . F 3 HOH B 60 660 112 HOH HOH . F 3 HOH B 61 661 127 HOH HOH . F 3 HOH B 62 662 18 HOH HOH . F 3 HOH B 63 663 85 HOH HOH . F 3 HOH B 64 664 202 HOH HOH . F 3 HOH B 65 665 219 HOH HOH . F 3 HOH B 66 666 45 HOH HOH . F 3 HOH B 67 667 122 HOH HOH . F 3 HOH B 68 668 114 HOH HOH . F 3 HOH B 69 669 15 HOH HOH . F 3 HOH B 70 670 158 HOH HOH . F 3 HOH B 71 671 137 HOH HOH . F 3 HOH B 72 672 191 HOH HOH . F 3 HOH B 73 673 98 HOH HOH . F 3 HOH B 74 674 149 HOH HOH . F 3 HOH B 75 675 72 HOH HOH . F 3 HOH B 76 676 86 HOH HOH . F 3 HOH B 77 677 77 HOH HOH . F 3 HOH B 78 678 171 HOH HOH . F 3 HOH B 79 679 177 HOH HOH . F 3 HOH B 80 680 203 HOH HOH . F 3 HOH B 81 681 122 HOH HOH . F 3 HOH B 82 682 87 HOH HOH . F 3 HOH B 83 683 197 HOH HOH . F 3 HOH B 84 684 41 HOH HOH . F 3 HOH B 85 685 28 HOH HOH . F 3 HOH B 86 686 110 HOH HOH . F 3 HOH B 87 687 168 HOH HOH . F 3 HOH B 88 688 178 HOH HOH . F 3 HOH B 89 689 46 HOH HOH . F 3 HOH B 90 690 55 HOH HOH . F 3 HOH B 91 691 33 HOH HOH . F 3 HOH B 92 692 69 HOH HOH . F 3 HOH B 93 693 173 HOH HOH . F 3 HOH B 94 694 45 HOH HOH . F 3 HOH B 95 695 83 HOH HOH . F 3 HOH B 96 696 136 HOH HOH . F 3 HOH B 97 697 50 HOH HOH . F 3 HOH B 98 698 111 HOH HOH . F 3 HOH B 99 699 141 HOH HOH . F 3 HOH B 100 700 64 HOH HOH . F 3 HOH B 101 701 183 HOH HOH . F 3 HOH B 102 702 116 HOH HOH . F 3 HOH B 103 703 66 HOH HOH . F 3 HOH B 104 704 11 HOH HOH . F 3 HOH B 105 705 78 HOH HOH . F 3 HOH B 106 706 40 HOH HOH . F 3 HOH B 107 707 134 HOH HOH . F 3 HOH B 108 708 249 HOH HOH . F 3 HOH B 109 709 15 HOH HOH . F 3 HOH B 110 710 253 HOH HOH . F 3 HOH B 111 711 244 HOH HOH . F 3 HOH B 112 712 254 HOH HOH . F 3 HOH B 113 713 64 HOH HOH . F 3 HOH B 114 714 192 HOH HOH . F 3 HOH B 115 715 252 HOH HOH . F 3 HOH B 116 716 247 HOH HOH . F 3 HOH B 117 717 255 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 . . . D 2 74.077 13.127 25.793 1 20 ? O4 DST 501 B 1 HETATM 2 P P1 DST . . . D 2 72.65 13.891 25.766 1 20 ? P1 DST 501 B 1 HETATM 3 O O6 DST . . . D 2 72.716 15.212 26.441 1 20 ? O6 DST 501 B 1 HETATM 4 O O5 DST . . . D 2 72.277 14.032 24.197 1 20 ? O5 DST 501 B 1 HETATM 5 O O2 DST . . . D 2 71.572 12.885 26.411 1 20 ? O2 DST 501 B 1 HETATM 6 P P3 DST . . . D 2 71.764 12.356 27.93 1 20 ? P3 DST 501 B 1 HETATM 7 O O8 DST . . . D 2 72.856 13.076 28.632 1 20 ? O8 DST 501 B 1 HETATM 8 O O7 DST . . . D 2 72.076 10.774 27.788 1 20 ? O7 DST 501 B 1 HETATM 9 S S9 DST . . . D 2 70.046 12.511 28.795 1 20 ? S9 DST 501 B 1 HETATM 10 C C10 DST . . . D 2 70.311 11.403 30.227 1 20 ? C10 DST 501 B 1 HETATM 11 C C11 DST . . . D 2 69.508 10.115 30.032 1 20 ? C11 DST 501 B 1 HETATM 12 C C12 DST . . . D 2 69.491 9.05 31.13 1 20 ? C12 DST 501 B 1 HETATM 13 C C13 DST . . . D 2 70.278 9.272 32.423 1 20 ? C13 DST 501 B 1 HETATM 14 C C14 DST . . . D 2 68.688 7.763 30.934 1 20 ? C14 DST 501 B 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #