data_5DYD # _model_server_result.job_id dt3IIHniJr5IVdLG8yGZnw _model_server_result.datetime_utc '2024-10-12 16:31:03' _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 5dyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":901}' # _entry.id 5DYD # _exptl.entry_id 5DYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 326.452 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4,4'-{[(3S)-3-(methylsulfanyl)cyclohexylidene]methanediyl}diphenol" _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 111.01 _cell.angle_gamma 90 _cell.entry_id 5DYD _cell.length_a 54.044 _cell.length_b 81.29 _cell.length_c 58.192 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _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 _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 ? 3 E N N ? 3 F N N # _chem_comp.formula 'C20 H22 O2 S' _chem_comp.formula_weight 326.452 _chem_comp.id 5K1 _chem_comp.mon_nstd_flag . _chem_comp.name "4,4'-{[(3S)-3-(methylsulfanyl)cyclohexylidene]methanediyl}diphenol" _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 O01 C02 5K1 sing 1 n n C02 C23 5K1 doub 2 n y C02 C03 5K1 sing 3 n y C23 C22 5K1 sing 4 n y C03 C04 5K1 doub 5 n y C22 C05 5K1 doub 6 n y C04 C05 5K1 sing 7 n y C05 C06 5K1 sing 8 n n C06 C07 5K1 sing 9 n n C06 C14 5K1 doub 10 n n C07 C13 5K1 doub 11 n y C07 C08 5K1 sing 12 n y C13 C12 5K1 sing 13 n y C08 C09 5K1 doub 14 n y C12 C10 5K1 doub 15 n y C09 C10 5K1 sing 16 n y C10 O11 5K1 sing 17 n n C15 C14 5K1 sing 18 n n C15 C16 5K1 sing 19 n n C14 C21 5K1 sing 20 n n C16 C17 5K1 sing 21 n n C21 C18 5K1 sing 22 n n C17 C18 5K1 sing 23 n n C18 S19 5K1 sing 24 n n S19 C20 5K1 sing 25 n n O01 H1 5K1 sing 26 n n C03 H2 5K1 sing 27 n n C04 H3 5K1 sing 28 n n C08 H5 5K1 sing 29 n n C09 H6 5K1 sing 30 n n O11 H7 5K1 sing 31 n n C12 H8 5K1 sing 32 n n C13 H9 5K1 sing 33 n n C15 H11 5K1 sing 34 n n C15 H12 5K1 sing 35 n n C16 H13 5K1 sing 36 n n C16 H14 5K1 sing 37 n n C17 H15 5K1 sing 38 n n C17 H16 5K1 sing 39 n n C18 H17 5K1 sing 40 n n C20 H18 5K1 sing 41 n n C20 H19 5K1 sing 42 n n C20 H20 5K1 sing 43 n n C21 H21 5K1 sing 44 n n C21 H22 5K1 sing 45 n n C22 H23 5K1 sing 46 n n C23 H24 5K1 sing 47 n n # _atom_sites.entry_id 5DYD _atom_sites.fract_transf_matrix[1][1] 0.018503 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007107 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012302 _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] 0.018408 _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 5K1 A 1 900 900 5K1 5K1 . F 3 5K1 B 1 901 901 5K1 5K1 . G 4 HOH A 1 1001 3 HOH HOH . G 4 HOH A 2 1002 1 HOH HOH . G 4 HOH A 3 1003 5 HOH HOH . G 4 HOH A 4 1004 2 HOH HOH . G 4 HOH A 5 1005 4 HOH HOH . G 4 HOH A 6 1006 32 HOH HOH . G 4 HOH A 7 1007 9 HOH HOH . G 4 HOH A 8 1008 8 HOH HOH . G 4 HOH A 9 1009 6 HOH HOH . G 4 HOH A 10 1010 11 HOH HOH . G 4 HOH A 11 1011 7 HOH HOH . G 4 HOH A 12 1012 10 HOH HOH . G 4 HOH A 13 1013 13 HOH HOH . G 4 HOH A 14 1014 12 HOH HOH . G 4 HOH A 15 1015 15 HOH HOH . G 4 HOH A 16 1016 34 HOH HOH . H 4 HOH B 1 1001 17 HOH HOH . H 4 HOH B 2 1002 18 HOH HOH . H 4 HOH B 3 1003 16 HOH HOH . H 4 HOH B 4 1004 33 HOH HOH . H 4 HOH B 5 1005 19 HOH HOH . H 4 HOH B 6 1006 23 HOH HOH . H 4 HOH B 7 1007 22 HOH HOH . H 4 HOH B 8 1008 21 HOH HOH . H 4 HOH B 9 1009 20 HOH HOH . H 4 HOH B 10 1010 24 HOH HOH . H 4 HOH B 11 1011 14 HOH HOH . H 4 HOH B 12 1012 25 HOH HOH . H 4 HOH B 13 1013 30 HOH HOH . H 4 HOH B 14 1014 26 HOH HOH . H 4 HOH B 15 1015 27 HOH HOH . H 4 HOH B 16 1016 28 HOH HOH . I 4 HOH C 1 701 29 HOH HOH . I 4 HOH C 2 702 31 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 O O01 5K1 . . . F 3 5.609 7.155 34.358 1 43.18 ? O01 5K1 901 B 1 HETATM 2 C C02 5K1 . . . F 3 6.859 6.791 33.924 1 43.06 ? C02 5K1 901 B 1 HETATM 3 C C03 5K1 . . . F 3 7.173 6.931 32.616 1 43.98 ? C03 5K1 901 B 1 HETATM 4 C C04 5K1 . . . F 3 8.409 6.565 32.169 1 43.83 ? C04 5K1 901 B 1 HETATM 5 C C05 5K1 . . . F 3 9.344 6.088 33.026 1 45.53 ? C05 5K1 901 B 1 HETATM 6 C C06 5K1 . . . F 3 10.68 5.69 32.469 1 49.78 ? C06 5K1 901 B 1 HETATM 7 C C07 5K1 . . . F 3 11.405 4.588 33.185 1 48.09 ? C07 5K1 901 B 1 HETATM 8 C C08 5K1 . . . F 3 10.973 3.307 33.009 1 47.03 ? C08 5K1 901 B 1 HETATM 9 C C09 5K1 . . . F 3 11.6 2.269 33.623 1 46.07 ? C09 5K1 901 B 1 HETATM 10 C C10 5K1 . . . F 3 12.674 2.52 34.41 1 46.38 ? C10 5K1 901 B 1 HETATM 11 O O11 5K1 . . . F 3 13.292 1.45 35.018 1 47.04 ? O11 5K1 901 B 1 HETATM 12 C C12 5K1 . . . F 3 13.135 3.797 34.59 1 46.22 ? C12 5K1 901 B 1 HETATM 13 C C13 5K1 . . . F 3 12.498 4.834 33.972 1 46.98 ? C13 5K1 901 B 1 HETATM 14 C C14 5K1 . . . F 3 11.632 6.796 32.099 1 53.75 ? C14 5K1 901 B 1 HETATM 15 C C15 5K1 . . . F 3 10.984 7.974 31.428 1 55.58 ? C15 5K1 901 B 1 HETATM 16 C C16 5K1 . . . F 3 12.019 9.039 31.212 1 56.44 ? C16 5K1 901 B 1 HETATM 17 C C17 5K1 . . . F 3 13.208 8.517 30.464 1 56.94 ? C17 5K1 901 B 1 HETATM 18 C C18 5K1 . . . F 3 13.724 7.254 31.072 1 56.39 ? C18 5K1 901 B 1 HETATM 19 S S19 5K1 . . . F 3 14.978 6.629 30.033 1 71.33 ? S19 5K1 901 B 1 HETATM 20 C C20 5K1 . . . F 3 16.086 5.595 30.897 1 55.03 ? C20 5K1 901 B 1 HETATM 21 C C21 5K1 . . . F 3 12.631 6.239 31.143 1 55.04 ? C21 5K1 901 B 1 HETATM 22 C C22 5K1 . . . F 3 9.025 5.948 34.343 1 44.48 ? C22 5K1 901 B 1 HETATM 23 C C23 5K1 . . . F 3 7.782 6.308 34.792 1 42.74 ? C23 5K1 901 B 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #