data_6KPF # _model_server_result.job_id 33EpK4W-fSKGO49SrGy58w _model_server_result.datetime_utc '2024-11-21 22:32:51' _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 6kpf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 6KPF # _exptl.entry_id 6KPF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 399.566 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]- 7-methyloctanenitrile' _entity.pdbx_number_of_molecules 1 _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 6KPF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KPF _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 # _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 D SG CYS 174 R CYS 174 1_555 D SG CYS 179 R CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 E SG CYS 22 S CYS 22 1_555 E SG CYS 96 S CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 E SG CYS 159 S CYS 147 1_555 E SG CYS 229 S CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? # _chem_comp.formula 'C25 H37 N O3' _chem_comp.formula_weight 399.566 _chem_comp.id E3R _chem_comp.mon_nstd_flag . _chem_comp.name '7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]- 7-methyloctanenitrile' _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 O3 C4 E3R sing 83 n n O2 C14 E3R sing 84 n n C14 C11 E3R sing 85 n n C4 C3 E3R doub 86 n y C4 C5 E3R sing 87 n y C3 C2 E3R sing 88 n y C19 C17 E3R sing 89 n n C10 C11 E3R sing 90 n n C10 C7 E3R sing 91 n n C11 C12 E3R sing 92 n n C7 C5 E3R sing 93 n n C7 C8 E3R sing 94 n n C5 C6 E3R doub 95 n y C20 C17 E3R sing 96 n n C2 C17 E3R sing 97 n n C2 C1 E3R doub 98 n y C17 C18 E3R sing 99 n n C12 C13 E3R sing 100 n n C6 C1 E3R sing 101 n y C6 O1 E3R sing 102 n n C16 C9 E3R sing 103 n n C8 C13 E3R sing 104 n n C8 C9 E3R sing 105 n n C18 C21 E3R sing 106 n n O1 C9 E3R sing 107 n n C21 C22 E3R sing 108 n n C9 C15 E3R sing 109 n n C22 C23 E3R sing 110 n n C23 C24 E3R sing 111 n n N1 C25 E3R trip 112 n n C25 C24 E3R sing 113 n n C1 H1 E3R sing 114 n n C3 H2 E3R sing 115 n n C10 H3 E3R sing 116 n n C10 H4 E3R sing 117 n n C11 H5 E3R sing 118 n n C12 H6 E3R sing 119 n n C12 H7 E3R sing 120 n n C13 H8 E3R sing 121 n n C13 H9 E3R sing 122 n n C14 H10 E3R sing 123 n n C14 H11 E3R sing 124 n n C15 H12 E3R sing 125 n n C15 H13 E3R sing 126 n n C15 H14 E3R sing 127 n n C16 H15 E3R sing 128 n n C16 H16 E3R sing 129 n n C16 H17 E3R sing 130 n n C18 H18 E3R sing 131 n n C18 H19 E3R sing 132 n n C19 H20 E3R sing 133 n n C19 H21 E3R sing 134 n n C19 H22 E3R sing 135 n n C20 H23 E3R sing 136 n n C20 H24 E3R sing 137 n n C20 H25 E3R sing 138 n n C21 H26 E3R sing 139 n n C21 H27 E3R sing 140 n n C22 H28 E3R sing 141 n n C22 H29 E3R sing 142 n n C23 H30 E3R sing 143 n n C23 H31 E3R sing 144 n n C24 H32 E3R sing 145 n n C24 H33 E3R sing 146 n n C7 H34 E3R sing 147 n n C8 H35 E3R sing 148 n n O2 H36 E3R sing 149 n n O3 H37 E3R sing 150 n n # _atom_sites.entry_id 6KPF _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 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id E3R _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _pdbx_nonpoly_scheme.pdb_mon_id E3R _pdbx_nonpoly_scheme.auth_mon_id AM3 _pdbx_nonpoly_scheme.pdb_ins_code . # 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 E3R . . . F 6 111.573 110.761 126.181 1 78.64 ? C1 E3R 401 R 1 HETATM 2 C C2 E3R . . . F 6 110.931 111.647 125.339 1 78.64 ? C2 E3R 401 R 1 HETATM 3 C C3 E3R . . . F 6 110.033 111.277 124.356 1 78.64 ? C3 E3R 401 R 1 HETATM 4 C C4 E3R . . . F 6 109.866 109.888 124.333 1 78.64 ? C4 E3R 401 R 1 HETATM 5 C C5 E3R . . . F 6 110.465 108.877 125.157 1 78.64 ? C5 E3R 401 R 1 HETATM 6 N N1 E3R . . . F 6 105.83 111.822 129.648 1 78.64 ? N1 E3R 401 R 1 HETATM 7 C C10 E3R . . . F 6 108.98 106.739 124.611 1 78.64 ? C10 E3R 401 R 1 HETATM 8 C C11 E3R . . . F 6 108.631 105.255 124.655 1 78.64 ? C11 E3R 401 R 1 HETATM 9 C C12 E3R . . . F 6 108.827 104.816 126.112 1 78.64 ? C12 E3R 401 R 1 HETATM 10 C C13 E3R . . . F 6 110.153 105.289 126.748 1 78.64 ? C13 E3R 401 R 1 HETATM 11 C C14 E3R . . . F 6 107.165 105.116 124.246 1 78.64 ? C14 E3R 401 R 1 HETATM 12 C C15 E3R . . . F 6 111.934 106.741 128.604 1 78.64 ? C15 E3R 401 R 1 HETATM 13 C C16 E3R . . . F 6 112.866 106.362 126.303 1 78.64 ? C16 E3R 401 R 1 HETATM 14 C C17 E3R . . . F 6 111.257 113.15 125.523 1 78.64 ? C17 E3R 401 R 1 HETATM 15 C C18 E3R . . . F 6 110.86 113.606 126.961 1 78.64 ? C18 E3R 401 R 1 HETATM 16 C C19 E3R . . . F 6 110.534 114.03 124.482 1 78.64 ? C19 E3R 401 R 1 HETATM 17 C C20 E3R . . . F 6 112.769 113.331 125.312 1 78.64 ? C20 E3R 401 R 1 HETATM 18 C C21 E3R . . . F 6 109.335 113.638 127.095 1 78.64 ? C21 E3R 401 R 1 HETATM 19 C C22 E3R . . . F 6 108.904 113.107 128.469 1 78.64 ? C22 E3R 401 R 1 HETATM 20 C C23 E3R . . . F 6 108.2 114.232 129.24 1 78.64 ? C23 E3R 401 R 1 HETATM 21 C C24 E3R . . . F 6 107.506 113.64 130.486 1 78.64 ? C24 E3R 401 R 1 HETATM 22 C C25 E3R . . . F 6 106.589 112.609 130.026 1 78.64 ? C25 E3R 401 R 1 HETATM 23 C C6 E3R . . . F 6 111.382 109.378 126.136 1 78.64 ? C6 E3R 401 R 1 HETATM 24 C C7 E3R . . . F 6 110.303 107.341 125.15 1 78.64 ? C7 E3R 401 R 1 HETATM 25 C C8 E3R . . . F 6 110.417 106.811 126.61 1 78.64 ? C8 E3R 401 R 1 HETATM 26 C C9 E3R . . . F 6 111.823 107.128 127.125 1 78.64 ? C9 E3R 401 R 1 HETATM 27 O O1 E3R . . . F 6 112.057 108.559 127.008 1 78.64 ? O1 E3R 401 R 1 HETATM 28 O O2 E3R . . . F 6 106.783 103.751 124.214 1 78.64 ? O2 E3R 401 R 1 HETATM 29 O O3 E3R . . . F 6 108.971 109.583 123.34 1 78.64 ? O3 E3R 401 R 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #