data_3KDP # _model_server_result.job_id glD3X9Lx1fNQhJW58Y20Xw _model_server_result.datetime_utc '2024-12-02 12:25:52' _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 3kdp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":3001}' # _entry.id 3KDP # _exptl.entry_id 3KDP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 386.654 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CHOLESTEROL _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 3KDP _cell.length_a 68.93 _cell.length_b 261.5 _cell.length_c 334.78 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KDP _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,K,L 1 1 D,E,F,M,N,O,P,Q,R 2 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 ? 7 L N N ? 7 R 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 B SG CYS 109 B CYS 126 1_555 B SG CYS 132 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 142 B CYS 159 1_555 B SG CYS 158 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 B SG CYS 196 B CYS 213 1_555 B SG CYS 259 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 E SG CYS 109 D CYS 126 1_555 E SG CYS 132 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 E SG CYS 142 D CYS 159 1_555 E SG CYS 158 D CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 E SG CYS 196 D CYS 213 1_555 E SG CYS 259 D CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A O VAL 304 A VAL 322 1_555 J RB RB . A RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.055 ? metalc ? metalc2 A O VAL 307 A VAL 325 1_555 J RB RB . A RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc3 A OE1 GLU 309 A GLU 327 1_555 J RB RB . A RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.093 ? metalc ? metalc4 A OD1 ASP 351 A ASP 369 1_555 G MG MF4 . A MF4 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc5 A OD2 ASP 351 A ASP 369 1_555 H MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc6 A O THR 353 A THR 371 1_555 H MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc7 A OD2 ASP 692 A ASP 710 1_555 H MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc8 A OG SER 757 A SER 775 1_555 I RB RB . A RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? metalc ? metalc9 A OD1 ASN 758 A ASN 776 1_555 I RB RB . A RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc10 A OD1 ASN 758 A ASN 776 1_555 J RB RB . A RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc11 A OE2 GLU 761 A GLU 779 1_555 I RB RB . A RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.192 ? metalc ? metalc12 A OE2 GLU 761 A GLU 779 1_555 J RB RB . A RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.188 ? metalc ? metalc13 A OD2 ASP 786 A ASP 804 1_555 I RB RB . A RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc14 A OD2 ASP 786 A ASP 804 1_555 J RB RB . A RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.036 ? metalc ? metalc15 D O VAL 304 C VAL 322 1_555 P RB RB . C RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.147 ? metalc ? metalc16 D OD1 ASP 351 C ASP 369 1_555 M MG MF4 . C MF4 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc17 D OD2 ASP 351 C ASP 369 1_555 N MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc18 D OD1 ASP 351 C ASP 369 1_555 N MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc19 D O THR 353 C THR 371 1_555 N MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc20 D OD2 ASP 692 C ASP 710 1_555 N MG MG . C MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc21 D OG SER 757 C SER 775 1_555 O RB RB . C RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc22 D OD1 ASN 758 C ASN 776 1_555 O RB RB . C RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc23 D OD1 ASN 758 C ASN 776 1_555 P RB RB . C RB 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc24 D OE2 GLU 761 C GLU 779 1_555 O RB RB . C RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.186 ? metalc ? metalc25 D OD2 ASP 786 C ASP 804 1_555 O RB RB . C RB 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? # _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 3KDP _atom_sites.fract_transf_matrix[1][1] 0.014507 _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] 0.003824 _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] 0.002987 _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 G 4 MF4 A 1 2001 2001 MF4 MF4 . H 5 MG A 1 2002 2002 MG MG . I 6 RB A 1 2003 2003 RB RB . J 6 RB A 1 2004 2004 RB RB . K 6 RB A 1 2005 2005 RB RB . L 7 CLR B 1 3001 3001 CLR CLR . M 4 MF4 C 1 2001 2001 MF4 MF4 . N 5 MG C 1 2002 2002 MG MG . O 6 RB C 1 2003 2003 RB RB . P 6 RB C 1 2004 2004 RB RB . Q 6 RB C 1 2005 2005 RB RB . R 7 CLR D 1 3001 3001 CLR CLR . # 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 . . . R 7 -21.056 -118.171 76.543 1 101.96 ? C1 CLR 3001 D 1 HETATM 2 C C2 CLR . . . R 7 -20.989 -118.751 75.122 1 101.95 ? C2 CLR 3001 D 1 HETATM 3 C C3 CLR . . . R 7 -19.732 -118.433 74.291 1 102.05 ? C3 CLR 3001 D 1 HETATM 4 C C4 CLR . . . R 7 -18.503 -118.104 75.184 1 102.06 ? C4 CLR 3001 D 1 HETATM 5 C C5 CLR . . . R 7 -18.653 -117.515 76.616 1 102.02 ? C5 CLR 3001 D 1 HETATM 6 C C6 CLR . . . R 7 -18.664 -115.991 76.651 1 101.89 ? C6 CLR 3001 D 1 HETATM 7 C C7 CLR . . . R 7 -19.074 -115.359 77.97 1 101.95 ? C7 CLR 3001 D 1 HETATM 8 C C8 CLR . . . R 7 -19.081 -116.355 79.115 1 101.96 ? C8 CLR 3001 D 1 HETATM 9 C C9 CLR . . . R 7 -20.09 -117.445 78.748 1 102.01 ? C9 CLR 3001 D 1 HETATM 10 C C10 CLR . . . R 7 -19.776 -118.17 77.401 1 101.96 ? C10 CLR 3001 D 1 HETATM 11 C C11 CLR . . . R 7 -20.343 -118.413 79.934 1 102.07 ? C11 CLR 3001 D 1 HETATM 12 C C12 CLR . . . R 7 -20.495 -117.819 81.353 1 102.06 ? C12 CLR 3001 D 1 HETATM 13 C C13 CLR . . . R 7 -19.571 -116.62 81.65 1 102.14 ? C13 CLR 3001 D 1 HETATM 14 C C14 CLR . . . R 7 -19.625 -115.694 80.394 1 102.04 ? C14 CLR 3001 D 1 HETATM 15 C C15 CLR . . . R 7 -19.151 -114.305 80.842 1 102.14 ? C15 CLR 3001 D 1 HETATM 16 C C16 CLR . . . R 7 -19.353 -114.291 82.37 1 102.21 ? C16 CLR 3001 D 1 HETATM 17 C C17 CLR . . . R 7 -20.053 -115.631 82.753 1 102.26 ? C17 CLR 3001 D 1 HETATM 18 C C18 CLR . . . R 7 -18.167 -117.103 81.992 1 102.06 ? C18 CLR 3001 D 1 HETATM 19 C C19 CLR . . . R 7 -19.244 -119.593 77.653 1 101.96 ? C19 CLR 3001 D 1 HETATM 20 C C20 CLR . . . R 7 -19.951 -116.008 84.248 1 102.32 ? C20 CLR 3001 D 1 HETATM 21 C C21 CLR . . . R 7 -20.851 -117.196 84.569 1 102.3 ? C21 CLR 3001 D 1 HETATM 22 C C22 CLR . . . R 7 -20.38 -114.816 85.133 1 102.32 ? C22 CLR 3001 D 1 HETATM 23 C C23 CLR . . . R 7 -20.828 -115.216 86.548 1 102.38 ? C23 CLR 3001 D 1 HETATM 24 C C24 CLR . . . R 7 -19.659 -115.237 87.57 1 102.47 ? C24 CLR 3001 D 1 HETATM 25 C C25 CLR . . . R 7 -19.928 -115.746 89.023 1 102.59 ? C25 CLR 3001 D 1 HETATM 26 C C26 CLR . . . R 7 -18.843 -116.745 89.441 1 102.57 ? C26 CLR 3001 D 1 HETATM 27 C C27 CLR . . . R 7 -20.065 -114.645 90.094 1 102.88 ? C27 CLR 3001 D 1 HETATM 28 O O1 CLR . . . R 7 -19.454 -119.545 73.434 1 102.22 ? O1 CLR 3001 D 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #