data_8PY4 # _model_server_result.job_id JPW0h60bdni2JFOkfdmmqQ _model_server_result.datetime_utc '2024-12-03 21:08:13' _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 8py4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":704}' # _entry.id 8PY4 # _exptl.entry_id 8PY4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 386.654 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CHOLESTEROL _entity.pdbx_number_of_molecules 10 _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 8PY4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PY4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,N,O,P,Q,R,S,T,U,V,W,X _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 ? _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 ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L N N ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n G NAG 1 G 1 NAG G 1 NAG 4 n G NAG 2 G 2 NAG G 2 NAG 4 n H NAG 1 H 1 NAG H 1 NAG 4 n H NAG 2 H 2 NAG H 2 NAG # 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 disulf ? disulf1 A SG CYS 22 D CYS 22 1_555 A SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 23 E CYS 23 1_555 B SG CYS 88 E CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 C SG CYS 22 F CYS 22 1_555 C SG CYS 96 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 D SG CYS 602 B CYS 592 1_555 D SG CYS 618 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 D SG CYS 613 B CYS 603 1_555 E SG CYS 613 A CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 E SG CYS 602 A CYS 592 1_555 E SG CYS 618 A CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 F SG CYS 23 C CYS 23 1_555 F SG CYS 88 C CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 D ND2 ASN 606 B ASN 596 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? covale ? covale2 E ND2 ASN 606 A ASN 596 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? covale ? covale3 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale4 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? # _chem_comp.formula 'C27 H46 O' _chem_comp.formula_weight 386.654 _chem_comp.id CLR _chem_comp.mon_nstd_flag . _chem_comp.name CHOLESTEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 CLR sing 70 n n C1 C10 CLR sing 71 n n C1 H11 CLR sing 72 n n C1 H12 CLR sing 73 n n C2 C3 CLR sing 74 n n C2 H21 CLR sing 75 n n C2 H22 CLR sing 76 n n C3 C4 CLR sing 77 n n C3 O1 CLR sing 78 n n C3 H3 CLR sing 79 n n C4 C5 CLR sing 80 n n C4 H41 CLR sing 81 n n C4 H42 CLR sing 82 n n C5 C6 CLR doub 83 n n C5 C10 CLR sing 84 n n C6 C7 CLR sing 85 n n C6 H6 CLR sing 86 n n C7 C8 CLR sing 87 n n C7 H71 CLR sing 88 n n C7 H72 CLR sing 89 n n C8 C9 CLR sing 90 n n C8 C14 CLR sing 91 n n C8 H8 CLR sing 92 n n C9 C10 CLR sing 93 n n C9 C11 CLR sing 94 n n C9 H9 CLR sing 95 n n C10 C19 CLR sing 96 n n C11 C12 CLR sing 97 n n C11 H111 CLR sing 98 n n C11 H112 CLR sing 99 n n C12 C13 CLR sing 100 n n C12 H121 CLR sing 101 n n C12 H122 CLR sing 102 n n C13 C14 CLR sing 103 n n C13 C17 CLR sing 104 n n C13 C18 CLR sing 105 n n C14 C15 CLR sing 106 n n C14 H14 CLR sing 107 n n C15 C16 CLR sing 108 n n C15 H151 CLR sing 109 n n C15 H152 CLR sing 110 n n C16 C17 CLR sing 111 n n C16 H161 CLR sing 112 n n C16 H162 CLR sing 113 n n C17 C20 CLR sing 114 n n C17 H17 CLR sing 115 n n C18 H181 CLR sing 116 n n C18 H182 CLR sing 117 n n C18 H183 CLR sing 118 n n C19 H191 CLR sing 119 n n C19 H192 CLR sing 120 n n C19 H193 CLR sing 121 n n C20 C21 CLR sing 122 n n C20 C22 CLR sing 123 n n C20 H20 CLR sing 124 n n C21 H211 CLR sing 125 n n C21 H212 CLR sing 126 n n C21 H213 CLR sing 127 n n C22 C23 CLR sing 128 n n C22 H221 CLR sing 129 n n C22 H222 CLR sing 130 n n C23 C24 CLR sing 131 n n C23 H231 CLR sing 132 n n C23 H232 CLR sing 133 n n C24 C25 CLR sing 134 n n C24 H241 CLR sing 135 n n C24 H242 CLR sing 136 n n C25 C26 CLR sing 137 n n C25 C27 CLR sing 138 n n C25 H25 CLR sing 139 n n C26 H261 CLR sing 140 n n C26 H262 CLR sing 141 n n C26 H263 CLR sing 142 n n C27 H271 CLR sing 143 n n C27 H272 CLR sing 144 n n C27 H273 CLR sing 145 n n O1 H1 CLR sing 146 n n # _atom_sites.entry_id 8PY4 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 5 CLR B 1 701 702 CLR CLR . J 5 CLR B 1 702 703 CLR CLR . K 5 CLR B 1 703 704 CLR CLR . L 5 CLR B 1 704 706 CLR CLR . M 5 CLR B 1 705 1201 CLR CLR . N 5 CLR A 1 701 702 CLR CLR . O 5 CLR A 1 702 703 CLR CLR . P 5 CLR A 1 703 704 CLR CLR . Q 5 CLR A 1 704 706 CLR CLR . R 5 CLR A 1 705 1201 CLR CLR . S 6 I3O A 1 706 1104 I3O LIG . T 6 I3O A 1 707 1104 I3O LIG . U 7 HOH E 1 301 45 HOH HOH . V 7 HOH B 1 801 39 HOH HOH . V 7 HOH B 2 802 2 HOH HOH . V 7 HOH B 3 803 9 HOH HOH . V 7 HOH B 4 804 21 HOH HOH . V 7 HOH B 5 805 35 HOH HOH . V 7 HOH B 6 806 41 HOH HOH . V 7 HOH B 7 807 12 HOH HOH . V 7 HOH B 8 808 7 HOH HOH . V 7 HOH B 9 809 48 HOH HOH . V 7 HOH B 10 810 37 HOH HOH . V 7 HOH B 11 811 22 HOH HOH . V 7 HOH B 12 812 24 HOH HOH . V 7 HOH B 13 813 20 HOH HOH . V 7 HOH B 14 814 31 HOH HOH . V 7 HOH B 15 815 50 HOH HOH . V 7 HOH B 16 816 5 HOH HOH . V 7 HOH B 17 817 51 HOH HOH . W 7 HOH A 1 801 26 HOH HOH . W 7 HOH A 2 802 10 HOH HOH . W 7 HOH A 3 803 1 HOH HOH . W 7 HOH A 4 804 30 HOH HOH . W 7 HOH A 5 805 40 HOH HOH . W 7 HOH A 6 806 11 HOH HOH . W 7 HOH A 7 807 8 HOH HOH . W 7 HOH A 8 808 29 HOH HOH . W 7 HOH A 9 809 28 HOH HOH . W 7 HOH A 10 810 27 HOH HOH . W 7 HOH A 11 811 25 HOH HOH . W 7 HOH A 12 812 32 HOH HOH . W 7 HOH A 13 813 49 HOH HOH . W 7 HOH A 14 814 6 HOH HOH . X 7 HOH C 1 301 47 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 C C1 CLR . . . L 5 94.611 124.109 142.378 1 51.61 ? C1 CLR 704 B 1 HETATM 2 C C2 CLR . . . L 5 94.077 123.744 143.763 1 51.61 ? C2 CLR 704 B 1 HETATM 3 C C3 CLR . . . L 5 93.375 122.372 143.77 1 51.61 ? C3 CLR 704 B 1 HETATM 4 C C4 CLR . . . L 5 94.404 121.332 143.28 1 51.61 ? C4 CLR 704 B 1 HETATM 5 C C5 CLR . . . L 5 95.055 121.645 141.941 1 51.61 ? C5 CLR 704 B 1 HETATM 6 C C6 CLR . . . L 5 95.074 120.695 140.989 1 51.61 ? C6 CLR 704 B 1 HETATM 7 C C7 CLR . . . L 5 95.585 120.963 139.568 1 51.61 ? C7 CLR 704 B 1 HETATM 8 C C8 CLR . . . L 5 96.472 122.24 139.518 1 51.61 ? C8 CLR 704 B 1 HETATM 9 C C9 CLR . . . L 5 95.784 123.398 140.292 1 51.61 ? C9 CLR 704 B 1 HETATM 10 C C10 CLR . . . L 5 95.609 123.078 141.795 1 51.61 ? C10 CLR 704 B 1 HETATM 11 C C11 CLR . . . L 5 96.462 124.751 140.028 1 51.61 ? C11 CLR 704 B 1 HETATM 12 C C12 CLR . . . L 5 96.606 125.076 138.531 1 51.61 ? C12 CLR 704 B 1 HETATM 13 C C13 CLR . . . L 5 97.42 123.95 137.833 1 51.61 ? C13 CLR 704 B 1 HETATM 14 C C14 CLR . . . L 5 96.614 122.634 138.066 1 51.61 ? C14 CLR 704 B 1 HETATM 15 C C15 CLR . . . L 5 97.251 121.576 137.105 1 51.61 ? C15 CLR 704 B 1 HETATM 16 C C16 CLR . . . L 5 97.743 122.468 135.884 1 51.61 ? C16 CLR 704 B 1 HETATM 17 C C17 CLR . . . L 5 97.359 123.971 136.274 1 51.61 ? C17 CLR 704 B 1 HETATM 18 C C18 CLR . . . L 5 98.868 123.822 138.324 1 51.61 ? C18 CLR 704 B 1 HETATM 19 C C19 CLR . . . L 5 96.988 123.216 142.507 1 51.61 ? C19 CLR 704 B 1 HETATM 20 C C20 CLR . . . L 5 98.304 124.944 135.575 1 51.61 ? C20 CLR 704 B 1 HETATM 21 C C21 CLR . . . L 5 98.036 126.443 135.844 1 51.61 ? C21 CLR 704 B 1 HETATM 22 C C22 CLR . . . L 5 98.077 124.679 134.047 1 51.61 ? C22 CLR 704 B 1 HETATM 23 C C23 CLR . . . L 5 99.233 125.206 133.19 1 51.61 ? C23 CLR 704 B 1 HETATM 24 C C24 CLR . . . L 5 98.542 126.16 132.146 1 51.61 ? C24 CLR 704 B 1 HETATM 25 C C25 CLR . . . L 5 99.631 126.881 131.32 1 51.61 ? C25 CLR 704 B 1 HETATM 26 C C26 CLR . . . L 5 98.909 127.627 130.165 1 51.61 ? C26 CLR 704 B 1 HETATM 27 C C27 CLR . . . L 5 100.586 127.768 132.155 1 51.61 ? C27 CLR 704 B 1 HETATM 28 O O1 CLR . . . L 5 92.788 122.017 145.014 1 51.61 ? O1 CLR 704 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #