data_9DNX # _model_server_result.job_id VYuSwlbkq5QohYschdKdhw _model_server_result.datetime_utc '2025-10-01 14:10:57' _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 9dnx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1003}' # _entry.id 9DNX # _exptl.entry_id 9DNX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 386.654 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CHOLESTEROL _entity.pdbx_number_of_molecules 4 _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 9DNX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DNX _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 ? _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,I,J,K,L,M,N _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 ? 4 G N N ? 4 H N N ? 4 L N N ? 4 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 disulf ? disulf1 A SG CYS 161 A CYS 161 1_555 A SG CYS 172 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 173 A CYS 173 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 463 A CYS 463 1_555 A SG CYS 472 A CYS 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 562 A CYS 562 1_555 A SG CYS 568 A CYS 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 B SG CYS 29 D CYS 29 1_555 B SG CYS 53 D CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 31 D CYS 31 1_555 B SG CYS 78 D CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf7 B SG CYS 33 D CYS 33 1_555 B SG CYS 76 D CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 55 D CYS 55 1_555 B SG CYS 73 D CYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 C SG CYS 29 B CYS 29 1_555 C SG CYS 53 B CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 C SG CYS 31 B CYS 31 1_555 C SG CYS 78 B CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf11 C SG CYS 33 B CYS 33 1_555 C SG CYS 76 B CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 C SG CYS 55 B CYS 55 1_555 C SG CYS 73 B CYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 D SG CYS 161 C CYS 161 1_555 D SG CYS 172 C CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 D SG CYS 173 C CYS 173 1_555 D SG CYS 187 C CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 D SG CYS 463 C CYS 463 1_555 D SG CYS 472 C CYS 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf16 D SG CYS 562 C CYS 562 1_555 D SG CYS 568 C CYS 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _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 224 n n C1 C10 CLR sing 225 n n C1 H11 CLR sing 226 n n C1 H12 CLR sing 227 n n C2 C3 CLR sing 228 n n C2 H21 CLR sing 229 n n C2 H22 CLR sing 230 n n C3 C4 CLR sing 231 n n C3 O1 CLR sing 232 n n C3 H3 CLR sing 233 n n C4 C5 CLR sing 234 n n C4 H41 CLR sing 235 n n C4 H42 CLR sing 236 n n C5 C6 CLR doub 237 n n C5 C10 CLR sing 238 n n C6 C7 CLR sing 239 n n C6 H6 CLR sing 240 n n C7 C8 CLR sing 241 n n C7 H71 CLR sing 242 n n C7 H72 CLR sing 243 n n C8 C9 CLR sing 244 n n C8 C14 CLR sing 245 n n C8 H8 CLR sing 246 n n C9 C10 CLR sing 247 n n C9 C11 CLR sing 248 n n C9 H9 CLR sing 249 n n C10 C19 CLR sing 250 n n C11 C12 CLR sing 251 n n C11 H111 CLR sing 252 n n C11 H112 CLR sing 253 n n C12 C13 CLR sing 254 n n C12 H121 CLR sing 255 n n C12 H122 CLR sing 256 n n C13 C14 CLR sing 257 n n C13 C17 CLR sing 258 n n C13 C18 CLR sing 259 n n C14 C15 CLR sing 260 n n C14 H14 CLR sing 261 n n C15 C16 CLR sing 262 n n C15 H151 CLR sing 263 n n C15 H152 CLR sing 264 n n C16 C17 CLR sing 265 n n C16 H161 CLR sing 266 n n C16 H162 CLR sing 267 n n C17 C20 CLR sing 268 n n C17 H17 CLR sing 269 n n C18 H181 CLR sing 270 n n C18 H182 CLR sing 271 n n C18 H183 CLR sing 272 n n C19 H191 CLR sing 273 n n C19 H192 CLR sing 274 n n C19 H193 CLR sing 275 n n C20 C21 CLR sing 276 n n C20 C22 CLR sing 277 n n C20 H20 CLR sing 278 n n C21 H211 CLR sing 279 n n C21 H212 CLR sing 280 n n C21 H213 CLR sing 281 n n C22 C23 CLR sing 282 n n C22 H221 CLR sing 283 n n C22 H222 CLR sing 284 n n C23 C24 CLR sing 285 n n C23 H231 CLR sing 286 n n C23 H232 CLR sing 287 n n C24 C25 CLR sing 288 n n C24 H241 CLR sing 289 n n C24 H242 CLR sing 290 n n C25 C26 CLR sing 291 n n C25 C27 CLR sing 292 n n C25 H25 CLR sing 293 n n C26 H261 CLR sing 294 n n C26 H262 CLR sing 295 n n C26 H263 CLR sing 296 n n C27 H271 CLR sing 297 n n C27 H272 CLR sing 298 n n C27 H273 CLR sing 299 n n O1 H1 CLR sing 300 n n # _atom_sites.entry_id 9DNX _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 E 3 CL A 1 1001 1001 CL CL ? F 3 CL A 1 1002 1002 CL CL ? G 4 CLR A 1 1003 1003 CLR CLR ? H 4 CLR A 1 1004 1004 CLR CLR ? I 5 A1A8I A 1 1005 1005 A1A8I P35 ? J 3 CL C 1 1001 1001 CL CL ? K 3 CL C 1 1002 1002 CL CL ? L 4 CLR C 1 1003 1003 CLR CLR ? M 4 CLR C 1 1004 1004 CLR CLR ? N 5 A1A8I C 1 1005 1005 A1A8I P35 ? # 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 4 158.832 125.239 133.523 1 55.45 ? C1 CLR 1003 C 1 HETATM 2 C C2 CLR . . . L 4 158.692 125.514 132.031 1 56.64 ? C2 CLR 1003 C 1 HETATM 3 C C3 CLR . . . L 4 159.885 124.963 131.276 1 60.34 ? C3 CLR 1003 C 1 HETATM 4 C C4 CLR . . . L 4 160.03 123.469 131.554 1 57.38 ? C4 CLR 1003 C 1 HETATM 5 C C5 CLR . . . L 4 160.081 123.161 133.028 1 53.71 ? C5 CLR 1003 C 1 HETATM 6 C C6 CLR . . . L 4 161.076 122.431 133.528 1 56.18 ? C6 CLR 1003 C 1 HETATM 7 C C7 CLR . . . L 4 161.206 122.024 134.958 1 56.66 ? C7 CLR 1003 C 1 HETATM 8 C C8 CLR . . . L 4 159.939 122.276 135.767 1 56.02 ? C8 CLR 1003 C 1 HETATM 9 C C9 CLR . . . L 4 159.33 123.635 135.394 1 55.27 ? C9 CLR 1003 C 1 HETATM 10 C C10 CLR . . . L 4 158.971 123.745 133.886 1 52.61 ? C10 CLR 1003 C 1 HETATM 11 C C11 CLR . . . L 4 158.174 123.995 136.335 1 52.4 ? C11 CLR 1003 C 1 HETATM 12 C C12 CLR . . . L 4 158.53 123.909 137.821 1 52.44 ? C12 CLR 1003 C 1 HETATM 13 C C13 CLR . . . L 4 159.072 122.528 138.196 1 57.56 ? C13 CLR 1003 C 1 HETATM 14 C C14 CLR . . . L 4 160.257 122.262 137.253 1 57.73 ? C14 CLR 1003 C 1 HETATM 15 C C15 CLR . . . L 4 160.932 121.028 137.835 1 57.77 ? C15 CLR 1003 C 1 HETATM 16 C C16 CLR . . . L 4 160.782 121.232 139.355 1 55.96 ? C16 CLR 1003 C 1 HETATM 17 C C17 CLR . . . L 4 159.793 122.414 139.566 1 54.14 ? C17 CLR 1003 C 1 HETATM 18 C C18 CLR . . . L 4 157.983 121.456 138.08 1 57.56 ? C18 CLR 1003 C 1 HETATM 19 C C19 CLR . . . L 4 157.665 123.009 133.548 1 57.82 ? C19 CLR 1003 C 1 HETATM 20 C C20 CLR . . . L 4 158.971 122.251 140.855 1 53.16 ? C20 CLR 1003 C 1 HETATM 21 C C21 CLR . . . L 4 157.806 123.233 140.96 1 55.02 ? C21 CLR 1003 C 1 HETATM 22 C C22 CLR . . . L 4 159.892 122.392 142.076 1 55.01 ? C22 CLR 1003 C 1 HETATM 23 C C23 CLR . . . L 4 159.291 121.968 143.412 1 54.25 ? C23 CLR 1003 C 1 HETATM 24 C C24 CLR . . . L 4 160.306 122.061 144.546 1 57.63 ? C24 CLR 1003 C 1 HETATM 25 C C25 CLR . . . L 4 159.723 121.921 145.954 1 57.53 ? C25 CLR 1003 C 1 HETATM 26 C C26 CLR . . . L 4 158.91 123.162 146.312 1 56.55 ? C26 CLR 1003 C 1 HETATM 27 C C27 CLR . . . L 4 160.802 121.675 147.003 1 56.89 ? C27 CLR 1003 C 1 HETATM 28 O O1 CLR . . . L 4 159.706 125.228 129.9 1 59.82 ? O1 CLR 1003 C 1 HETATM 29 H H11 CLR . . . L 4 158.057 125.598 133.982 1 53.63 ? H11 CLR 1003 C 1 HETATM 30 H H12 CLR . . . L 4 159.599 125.728 133.858 1 53.62 ? H12 CLR 1003 C 1 HETATM 31 H H21 CLR . . . L 4 158.62 126.471 131.888 1 53.73 ? H21 CLR 1003 C 1 HETATM 32 H H22 CLR . . . L 4 157.877 125.118 131.685 1 53.24 ? H22 CLR 1003 C 1 HETATM 33 H H3 CLR . . . L 4 160.682 125.409 131.603 1 54.22 ? H3 CLR 1003 C 1 HETATM 34 H H41 CLR . . . L 4 160.83 123.127 131.125 1 53.82 ? H41 CLR 1003 C 1 HETATM 35 H H42 CLR . . . L 4 159.281 123.014 131.14 1 53.71 ? H42 CLR 1003 C 1 HETATM 36 H H6 CLR . . . L 4 161.782 122.202 132.968 1 53.98 ? H6 CLR 1003 C 1 HETATM 37 H H71 CLR . . . L 4 161.951 122.501 135.356 1 54.09 ? H71 CLR 1003 C 1 HETATM 38 H H72 CLR . . . L 4 161.451 121.087 135.003 1 53.67 ? H72 CLR 1003 C 1 HETATM 39 H H8 CLR . . . L 4 159.303 121.573 135.563 1 53.1 ? H8 CLR 1003 C 1 HETATM 40 H H9 CLR . . . L 4 160.031 124.287 135.551 1 53.8 ? H9 CLR 1003 C 1 HETATM 41 H H111 CLR . . . L 4 157.415 123.413 136.172 1 53.36 ? H111 CLR 1003 C 1 HETATM 42 H H112 CLR . . . L 4 157.86 124.893 136.142 1 52.88 ? H112 CLR 1003 C 1 HETATM 43 H H121 CLR . . . L 4 157.74 124.09 138.352 1 53.01 ? H121 CLR 1003 C 1 HETATM 44 H H122 CLR . . . L 4 159.163 124.615 138.024 1 53.43 ? H122 CLR 1003 C 1 HETATM 45 H H14 CLR . . . L 4 160.869 123.001 137.394 1 53.93 ? H14 CLR 1003 C 1 HETATM 46 H H151 CLR . . . L 4 161.859 120.95 137.561 1 53.84 ? H151 CLR 1003 C 1 HETATM 47 H H152 CLR . . . L 4 160.486 120.22 137.539 1 54.09 ? H152 CLR 1003 C 1 HETATM 48 H H161 CLR . . . L 4 161.64 121.416 139.77 1 53.59 ? H161 CLR 1003 C 1 HETATM 49 H H162 CLR . . . L 4 160.44 120.433 139.784 1 53.88 ? H162 CLR 1003 C 1 HETATM 50 H H17 CLR . . . L 4 160.31 123.229 139.665 1 53.6 ? H17 CLR 1003 C 1 HETATM 51 H H181 CLR . . . L 4 158.236 120.616 138.495 1 54.24 ? H181 CLR 1003 C 1 HETATM 52 H H182 CLR . . . L 4 157.757 121.258 137.158 1 53.44 ? H182 CLR 1003 C 1 HETATM 53 H H183 CLR . . . L 4 157.164 121.745 138.511 1 53.9 ? H183 CLR 1003 C 1 HETATM 54 H H191 CLR . . . L 4 157.66 122.106 133.903 1 53.89 ? H191 CLR 1003 C 1 HETATM 55 H H192 CLR . . . L 4 157.534 122.938 132.59 1 54.64 ? H192 CLR 1003 C 1 HETATM 56 H H193 CLR . . . L 4 156.892 123.461 133.922 1 54.32 ? H193 CLR 1003 C 1 HETATM 57 H H20 CLR . . . L 4 158.61 121.351 140.865 1 52.61 ? H20 CLR 1003 C 1 HETATM 58 H H211 CLR . . . L 4 157.359 123.153 141.816 1 53.38 ? H211 CLR 1003 C 1 HETATM 59 H H212 CLR . . . L 4 157.14 123.085 140.272 1 53.2 ? H212 CLR 1003 C 1 HETATM 60 H H213 CLR . . . L 4 158.104 124.151 140.866 1 52.46 ? H213 CLR 1003 C 1 HETATM 61 H H221 CLR . . . L 4 160.189 123.313 142.138 1 53.62 ? H221 CLR 1003 C 1 HETATM 62 H H222 CLR . . . L 4 160.697 121.868 141.941 1 53.64 ? H222 CLR 1003 C 1 HETATM 63 H H231 CLR . . . L 4 158.969 121.055 143.345 1 53.18 ? H231 CLR 1003 C 1 HETATM 64 H H232 CLR . . . L 4 158.516 122.511 143.624 1 52.55 ? H232 CLR 1003 C 1 HETATM 65 H H241 CLR . . . L 4 160.779 122.905 144.484 1 54.11 ? H241 CLR 1003 C 1 HETATM 66 H H242 CLR . . . L 4 160.977 121.372 144.419 1 53.72 ? H242 CLR 1003 C 1 HETATM 67 H H25 CLR . . . L 4 159.122 121.159 145.953 1 52.79 ? H25 CLR 1003 C 1 HETATM 68 H H261 CLR . . . L 4 158.651 123.159 147.247 1 52.72 ? H261 CLR 1003 C 1 HETATM 69 H H262 CLR . . . L 4 158.099 123.223 145.783 1 52.27 ? H262 CLR 1003 C 1 HETATM 70 H H263 CLR . . . L 4 159.425 123.968 146.154 1 52.97 ? H263 CLR 1003 C 1 HETATM 71 H H271 CLR . . . L 4 160.408 121.583 147.885 1 52.97 ? H271 CLR 1003 C 1 HETATM 72 H H272 CLR . . . L 4 161.448 122.398 147.044 1 54.08 ? H272 CLR 1003 C 1 HETATM 73 H H273 CLR . . . L 4 161.293 120.86 146.816 1 53.44 ? H273 CLR 1003 C 1 HETATM 74 H H1 CLR . . . L 4 160.348 124.867 129.476 1 54.46 ? H1 CLR 1003 C 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 74 #