data_1YST # _model_server_result.job_id qQXj7rD0SlmrisyHC_OWrQ _model_server_result.datetime_utc '2025-03-06 07:48:27' _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 1yst # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":311}' # _entry.id 1YST # _exptl.entry_id 1YST _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 863.343 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description UBIQUINONE-10 _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 1YST _cell.length_a 143.7 _cell.length_b 139.8 _cell.length_c 78.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YST _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 6 G N N ? 6 M 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 NE2 HIS 153 L HIS 153 1_555 E MG BCL . L BCL 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 A NE2 HIS 173 L HIS 173 1_555 D MG BCL . L BCL 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc3 A NE2 HIS 190 L HIS 190 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc4 A NE2 HIS 230 L HIS 230 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc5 B NE2 HIS 182 M HIS 182 1_555 I MG BCL . M BCL 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc6 B NE2 HIS 202 M HIS 202 1_555 J MG BCL . M BCL 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc7 B NE2 HIS 219 M HIS 219 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc8 B OE1 GLU 234 M GLU 234 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc9 B OE2 GLU 234 M GLU 234 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc10 B NE2 HIS 266 M HIS 266 1_555 H MN MN . M MN 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _chem_comp.formula 'C59 H90 O4' _chem_comp.formula_weight 863.343 _chem_comp.id U10 _chem_comp.mon_nstd_flag . _chem_comp.name UBIQUINONE-10 _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Coenzyme Q10' # 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 C1 C2 U10 sing 751 n n C1 C6 U10 doub 752 n n C1 C1M U10 sing 753 n n C2 C3 U10 sing 754 n n C2 O2 U10 doub 755 n n C3 C4 U10 doub 756 n n C3 O3 U10 sing 757 n n C4 C5 U10 sing 758 n n C4 O4 U10 sing 759 n n C5 C6 U10 sing 760 n n C5 O5 U10 doub 761 n n C6 C7 U10 sing 762 n n C1M H1M1 U10 sing 763 n n C1M H1M2 U10 sing 764 n n C1M H1M3 U10 sing 765 n n C3M O3 U10 sing 766 n n C3M H3M1 U10 sing 767 n n C3M H3M2 U10 sing 768 n n C3M H3M3 U10 sing 769 n n C4M O4 U10 sing 770 n n C4M H4M1 U10 sing 771 n n C4M H4M2 U10 sing 772 n n C4M H4M3 U10 sing 773 n n C7 C8 U10 sing 774 n n C7 H71 U10 sing 775 n n C7 H72 U10 sing 776 n n C8 C9 U10 doub 777 e n C8 H8 U10 sing 778 n n C9 C10 U10 sing 779 n n C9 C11 U10 sing 780 n n C10 H101 U10 sing 781 n n C10 H102 U10 sing 782 n n C10 H103 U10 sing 783 n n C11 C12 U10 sing 784 n n C11 H111 U10 sing 785 n n C11 H112 U10 sing 786 n n C12 C13 U10 sing 787 n n C12 H121 U10 sing 788 n n C12 H122 U10 sing 789 n n C13 C14 U10 doub 790 e n C13 H13 U10 sing 791 n n C14 C15 U10 sing 792 n n C14 C16 U10 sing 793 n n C15 H151 U10 sing 794 n n C15 H152 U10 sing 795 n n C15 H153 U10 sing 796 n n C16 C17 U10 sing 797 n n C16 H161 U10 sing 798 n n C16 H162 U10 sing 799 n n C17 C18 U10 sing 800 n n C17 H171 U10 sing 801 n n C17 H172 U10 sing 802 n n C18 C19 U10 doub 803 e n C18 H18 U10 sing 804 n n C19 C20 U10 sing 805 n n C19 C21 U10 sing 806 n n C20 H201 U10 sing 807 n n C20 H202 U10 sing 808 n n C20 H203 U10 sing 809 n n C21 C22 U10 sing 810 n n C21 H211 U10 sing 811 n n C21 H212 U10 sing 812 n n C22 C23 U10 sing 813 n n C22 H221 U10 sing 814 n n C22 H222 U10 sing 815 n n C23 C24 U10 doub 816 e n C23 H23 U10 sing 817 n n C24 C25 U10 sing 818 n n C24 C26 U10 sing 819 n n C25 H251 U10 sing 820 n n C25 H252 U10 sing 821 n n C25 H253 U10 sing 822 n n C26 C27 U10 sing 823 n n C26 H261 U10 sing 824 n n C26 H262 U10 sing 825 n n C27 C28 U10 sing 826 n n C27 H271 U10 sing 827 n n C27 H272 U10 sing 828 n n C28 C29 U10 doub 829 e n C28 H28 U10 sing 830 n n C29 C30 U10 sing 831 n n C29 C31 U10 sing 832 n n C30 H301 U10 sing 833 n n C30 H302 U10 sing 834 n n C30 H303 U10 sing 835 n n C31 C32 U10 sing 836 n n C31 H311 U10 sing 837 n n C31 H312 U10 sing 838 n n C32 C33 U10 sing 839 n n C32 H321 U10 sing 840 n n C32 H322 U10 sing 841 n n C33 C34 U10 doub 842 e n C33 H33 U10 sing 843 n n C34 C35 U10 sing 844 n n C34 C36 U10 sing 845 n n C35 H351 U10 sing 846 n n C35 H352 U10 sing 847 n n C35 H353 U10 sing 848 n n C36 C37 U10 sing 849 n n C36 H361 U10 sing 850 n n C36 H362 U10 sing 851 n n C37 C38 U10 sing 852 n n C37 H371 U10 sing 853 n n C37 H372 U10 sing 854 n n C38 C39 U10 doub 855 e n C38 H38 U10 sing 856 n n C39 C40 U10 sing 857 n n C39 C41 U10 sing 858 n n C40 H401 U10 sing 859 n n C40 H402 U10 sing 860 n n C40 H403 U10 sing 861 n n C41 C42 U10 sing 862 n n C41 H411 U10 sing 863 n n C41 H412 U10 sing 864 n n C42 C43 U10 sing 865 n n C42 H421 U10 sing 866 n n C42 H422 U10 sing 867 n n C43 C44 U10 doub 868 e n C43 H43 U10 sing 869 n n C44 C45 U10 sing 870 n n C44 C46 U10 sing 871 n n C45 H451 U10 sing 872 n n C45 H452 U10 sing 873 n n C45 H453 U10 sing 874 n n C46 C47 U10 sing 875 n n C46 H461 U10 sing 876 n n C46 H462 U10 sing 877 n n C47 C48 U10 sing 878 n n C47 H471 U10 sing 879 n n C47 H472 U10 sing 880 n n C48 C49 U10 doub 881 e n C48 H48 U10 sing 882 n n C49 C50 U10 sing 883 n n C49 C51 U10 sing 884 n n C50 H501 U10 sing 885 n n C50 H502 U10 sing 886 n n C50 H503 U10 sing 887 n n C51 C52 U10 sing 888 n n C51 H511 U10 sing 889 n n C51 H512 U10 sing 890 n n C52 C53 U10 sing 891 n n C52 H521 U10 sing 892 n n C52 H522 U10 sing 893 n n C53 C54 U10 doub 894 n n C53 H53 U10 sing 895 n n C54 C55 U10 sing 896 n n C54 C56 U10 sing 897 n n C55 H551 U10 sing 898 n n C55 H552 U10 sing 899 n n C55 H553 U10 sing 900 n n C56 H561 U10 sing 901 n n C56 H562 U10 sing 902 n n C56 H563 U10 sing 903 n n # _atom_sites.entry_id 1YST _atom_sites.fract_transf_matrix[1][1] 0.006959 _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] 0.007153 _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] 0.012715 _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 D 4 BCL L 1 274 2 BCL BCL . E 4 BCL L 1 275 4 BCL BCL . F 5 BPH L 1 276 6 BPH BPH . G 6 U10 L 1 277 10 U10 U10 . H 7 MN M 1 306 8 MN MN . I 4 BCL M 1 307 1 BCL BCL . J 4 BCL M 1 308 3 BCL BCL . K 5 BPH M 1 309 5 BPH BPH . L 8 SPO M 1 310 7 SPO SPO . M 6 U10 M 1 311 9 U10 U10 . # 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 C C1 U10 . . . M 6 -9.644 -37.712 -12.92 1 38.7 ? C1 U10 311 M 1 HETATM 2 C C2 U10 . . . M 6 -8.261 -37.832 -13.419 1 39.36 ? C2 U10 311 M 1 HETATM 3 C C3 U10 . . . M 6 -8.064 -37.668 -14.909 1 39.41 ? C3 U10 311 M 1 HETATM 4 C C4 U10 . . . M 6 -9.053 -37.408 -15.736 1 39.92 ? C4 U10 311 M 1 HETATM 5 C C5 U10 . . . M 6 -10.486 -37.275 -15.274 1 44.32 ? C5 U10 311 M 1 HETATM 6 C C6 U10 . . . M 6 -10.716 -37.453 -13.811 1 41.82 ? C6 U10 311 M 1 HETATM 7 C C1M U10 . . . M 6 -9.805 -37.888 -11.44 1 38.68 ? C1M U10 311 M 1 HETATM 8 C C3M U10 . . . M 6 -5.917 -36.835 -14.945 1 46.73 ? C3M U10 311 M 1 HETATM 9 C C4M U10 . . . M 6 -8.065 -38.437 -17.579 1 40.18 ? C4M U10 311 M 1 HETATM 10 C C7 U10 . . . M 6 -12.113 -37.371 -13.383 1 41.72 ? C7 U10 311 M 1 HETATM 11 C C8 U10 . . . M 6 -12.673 -36.058 -13.231 1 36.15 ? C8 U10 311 M 1 HETATM 12 C C9 U10 . . . M 6 -13.43 -35.423 -13.968 1 30.09 ? C9 U10 311 M 1 HETATM 13 C C10 U10 . . . M 6 -13.939 -35.929 -15.255 1 26.04 ? C10 U10 311 M 1 HETATM 14 C C11 U10 . . . M 6 -13.908 -34.047 -13.599 1 33.11 ? C11 U10 311 M 1 HETATM 15 C C12 U10 . . . M 6 -15.417 -33.947 -13.302 1 31.07 ? C12 U10 311 M 1 HETATM 16 C C13 U10 . . . M 6 -16.028 -35.074 -12.428 1 23.76 ? C13 U10 311 M 1 HETATM 17 C C14 U10 . . . M 6 -17.305 -35.168 -11.899 1 24.14 ? C14 U10 311 M 1 HETATM 18 C C15 U10 . . . M 6 -18.409 -34.062 -12.062 1 13.73 ? C15 U10 311 M 1 HETATM 19 C C16 U10 . . . M 6 -17.76 -36.39 -11.038 1 28.73 ? C16 U10 311 M 1 HETATM 20 C C17 U10 . . . M 6 -19.263 -36.794 -11.217 1 39.14 ? C17 U10 311 M 1 HETATM 21 C C18 U10 . . . M 6 -19.691 -37.877 -12.445 1 38.42 ? C18 U10 311 M 1 HETATM 22 C C19 U10 . . . M 6 -20.671 -38.439 -12.311 1 40.52 ? C19 U10 311 M 1 HETATM 23 C C20 U10 . . . M 6 -22.022 -38.012 -11.684 1 40.32 ? C20 U10 311 M 1 HETATM 24 C C21 U10 . . . M 6 -20.855 -39.6 -13.408 1 45.67 ? C21 U10 311 M 1 HETATM 25 C C22 U10 . . . M 6 -21.465 -40.91 -12.757 1 51.23 ? C22 U10 311 M 1 HETATM 26 C C23 U10 . . . M 6 -21.698 -42.275 -13.714 1 50.25 ? C23 U10 311 M 1 HETATM 27 C C24 U10 . . . M 6 -22.362 -42.446 -14.98 1 52.93 ? C24 U10 311 M 1 HETATM 28 C C25 U10 . . . M 6 -23.041 -41.294 -15.776 1 55.99 ? C25 U10 311 M 1 HETATM 29 C C26 U10 . . . M 6 -22.498 -43.81 -15.708 1 51.9 ? C26 U10 311 M 1 HETATM 30 C C27 U10 . . . M 6 -23.115 -43.654 -17.109 1 53.64 ? C27 U10 311 M 1 HETATM 31 C C28 U10 . . . M 6 -24.504 -44.372 -17.351 1 55.73 ? C28 U10 311 M 1 HETATM 32 C C29 U10 . . . M 6 -25.416 -44.285 -18.491 1 61.4 ? C29 U10 311 M 1 HETATM 33 C C30 U10 . . . M 6 -25.18 -43.411 -19.74 1 56.67 ? C30 U10 311 M 1 HETATM 34 C C31 U10 . . . M 6 -26.741 -45.103 -18.609 1 66.53 ? C31 U10 311 M 1 HETATM 35 C C32 U10 . . . M 6 -27.38 -45.081 -19.991 1 70.42 ? C32 U10 311 M 1 HETATM 36 C C33 U10 . . . M 6 -26.368 -45.432 -21.225 1 75.19 ? C33 U10 311 M 1 HETATM 37 C C34 U10 . . . M 6 -25.625 -46.649 -21.598 1 72.95 ? C34 U10 311 M 1 HETATM 38 C C35 U10 . . . M 6 -25.64 -48.003 -20.794 1 68.39 ? C35 U10 311 M 1 HETATM 39 C C36 U10 . . . M 6 -24.717 -46.703 -22.891 1 68.12 ? C36 U10 311 M 1 HETATM 40 C C37 U10 . . . M 6 -25.423 -46.297 -24.165 1 63.52 ? C37 U10 311 M 1 HETATM 41 C C38 U10 . . . M 6 -24.469 -45.607 -25.206 1 62.38 ? C38 U10 311 M 1 HETATM 42 C C39 U10 . . . M 6 -24.484 -45.569 -26.647 1 60.5 ? C39 U10 311 M 1 HETATM 43 C C40 U10 . . . M 6 -25.441 -46.382 -27.549 1 57.52 ? C40 U10 311 M 1 HETATM 44 C C41 U10 . . . M 6 -23.547 -44.676 -27.46 1 60.37 ? C41 U10 311 M 1 HETATM 45 C C42 U10 . . . M 6 -23.756 -43.197 -27.154 1 64.97 ? C42 U10 311 M 1 HETATM 46 C C43 U10 . . . M 6 -23.436 -42.829 -25.596 1 64.04 ? C43 U10 311 M 1 HETATM 47 C C44 U10 . . . M 6 -23.465 -41.603 -24.86 1 60.83 ? C44 U10 311 M 1 HETATM 48 C C45 U10 . . . M 6 -23.847 -40.189 -25.455 1 55.87 ? C45 U10 311 M 1 HETATM 49 C C46 U10 . . . M 6 -23.105 -41.556 -23.353 1 61.14 ? C46 U10 311 M 1 HETATM 50 C C47 U10 . . . M 6 -22.77 -40.131 -22.873 1 58.52 ? C47 U10 311 M 1 HETATM 51 C C48 U10 . . . M 6 -21.607 -39.468 -23.677 1 57.28 ? C48 U10 311 M 1 HETATM 52 C C49 U10 . . . M 6 -20.858 -38.273 -23.452 1 62.25 ? C49 U10 311 M 1 HETATM 53 C C50 U10 . . . M 6 -21.076 -37.308 -22.235 1 62.54 ? C50 U10 311 M 1 HETATM 54 C C51 U10 . . . M 6 -19.689 -37.769 -24.402 1 64.61 ? C51 U10 311 M 1 HETATM 55 O O2 U10 . . . M 6 -7.347 -38.057 -12.677 1 38.76 ? O2 U10 311 M 1 HETATM 56 O O3 U10 . . . M 6 -6.827 -37.795 -15.413 1 40.58 ? O3 U10 311 M 1 HETATM 57 O O4 U10 . . . M 6 -8.758 -37.288 -17.011 1 39.61 ? O4 U10 311 M 1 HETATM 58 O O5 U10 . . . M 6 -11.427 -37.049 -16.064 1 49.88 ? O5 U10 311 M 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 58 #