data_5DYD # _model_server_result.job_id 1rCBOQ9epRF-7KOkalaNRg _model_server_result.datetime_utc '2024-10-12 16:37:47' _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":"E","auth_seq_id":900}' # _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 . . . E 3 16.442 -0.789 0.111 1 44.16 ? O01 5K1 900 A 1 HETATM 2 C C02 5K1 . . . E 3 17.03 -1.063 1.327 1 42.78 ? C02 5K1 900 A 1 HETATM 3 C C03 5K1 . . . E 3 16.275 -1.101 2.446 1 42.66 ? C03 5K1 900 A 1 HETATM 4 C C04 5K1 . . . E 3 16.859 -1.384 3.643 1 42.24 ? C04 5K1 900 A 1 HETATM 5 C C05 5K1 . . . E 3 18.195 -1.641 3.726 1 42.59 ? C05 5K1 900 A 1 HETATM 6 C C06 5K1 . . . E 3 18.815 -1.902 5.073 1 42.8 ? C06 5K1 900 A 1 HETATM 7 C C07 5K1 . . . E 3 20.276 -1.559 5.115 1 41.78 ? C07 5K1 900 A 1 HETATM 8 C C08 5K1 . . . E 3 20.679 -0.257 5.186 1 40.76 ? C08 5K1 900 A 1 HETATM 9 C C09 5K1 . . . E 3 22.009 0.052 5.225 1 40.42 ? C09 5K1 900 A 1 HETATM 10 C C10 5K1 . . . E 3 22.934 -0.94 5.205 1 41.16 ? C10 5K1 900 A 1 HETATM 11 O O11 5K1 . . . E 3 24.275 -0.645 5.249 1 41.61 ? O11 5K1 900 A 1 HETATM 12 C C12 5K1 . . . E 3 22.541 -2.238 5.15 1 40.91 ? C12 5K1 900 A 1 HETATM 13 C C13 5K1 . . . E 3 21.217 -2.543 5.098 1 41.21 ? C13 5K1 900 A 1 HETATM 14 C C14 5K1 . . . E 3 18.517 -3.24 5.7 1 43.25 ? C14 5K1 900 A 1 HETATM 15 C C15 5K1 . . . E 3 17.077 -3.623 5.556 1 43.67 ? C15 5K1 900 A 1 HETATM 16 C C16 5K1 . . . E 3 16.907 -5.032 6.044 1 44.1 ? C16 5K1 900 A 1 HETATM 17 C C17 5K1 . . . E 3 17.432 -5.225 7.431 1 43.84 ? C17 5K1 900 A 1 HETATM 18 C C18 5K1 . . . E 3 18.823 -4.683 7.548 1 43.59 ? C18 5K1 900 A 1 HETATM 19 S S19 5K1 . . . E 3 19.324 -4.85 9.211 1 52.87 ? S19 5K1 900 A 1 HETATM 20 C C20 5K1 . . . E 3 20.8 -3.984 9.503 1 47.42 ? C20 5K1 900 A 1 HETATM 21 C C21 5K1 . . . E 3 18.83 -3.241 7.161 1 42.72 ? C21 5K1 900 A 1 HETATM 22 C C22 5K1 . . . E 3 18.95 -1.598 2.591 1 42.93 ? C22 5K1 900 A 1 HETATM 23 C C23 5K1 . . . E 3 18.359 -1.32 1.396 1 41.92 ? C23 5K1 900 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 23 #