data_5DKE # _model_server_result.job_id xBWHt7-otjUQEmv31NHyCQ _model_server_result.datetime_utc '2024-11-29 04:17:24' _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 5dke # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 5DKE # _exptl.entry_id 5DKE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 352.425 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4,4'-[2-(naphthalen-2-yl)prop-1-ene-1,1-diyl]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 109.79 _cell.angle_gamma 90 _cell.entry_id 5DKE _cell.length_a 52.758 _cell.length_b 77.301 _cell.length_c 57.528 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DKE _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,J _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 'C25 H20 O2' _chem_comp.formula_weight 352.425 _chem_comp.id 5C8 _chem_comp.mon_nstd_flag . _chem_comp.name "4,4'-[2-(naphthalen-2-yl)prop-1-ene-1,1-diyl]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 O08 C07 5C8 sing 1 n n C09 C07 5C8 doub 2 n y C09 C10 5C8 sing 3 n y C07 C06 5C8 sing 4 n y C10 C04 5C8 doub 5 n y C06 C05 5C8 doub 6 n y C04 C05 5C8 sing 7 n y C04 C03 5C8 sing 8 n n C03 C11 5C8 sing 9 n n C03 C02 5C8 doub 10 n n C12 C11 5C8 doub 11 n y C12 C13 5C8 sing 12 n y C11 C17 5C8 sing 13 n y C13 C14 5C8 doub 14 n y C17 C16 5C8 doub 15 n y C14 C16 5C8 sing 16 n y C14 O15 5C8 sing 17 n n C01 C02 5C8 sing 18 n n C02 C18 5C8 sing 19 n n C18 C27 5C8 doub 20 n y C18 C19 5C8 sing 21 n y C27 C26 5C8 sing 22 n y C19 C20 5C8 doub 23 n y C26 C25 5C8 doub 24 n y C26 C21 5C8 sing 25 n y C25 C24 5C8 sing 26 n y C20 C21 5C8 sing 27 n y C21 C22 5C8 doub 28 n y C24 C23 5C8 doub 29 n y C22 C23 5C8 sing 30 n y C01 H1 5C8 sing 31 n n C01 H2 5C8 sing 32 n n C01 H3 5C8 sing 33 n n C05 H4 5C8 sing 34 n n C06 H5 5C8 sing 35 n n O08 H6 5C8 sing 36 n n C09 H7 5C8 sing 37 n n C10 H8 5C8 sing 38 n n C12 H9 5C8 sing 39 n n C13 H10 5C8 sing 40 n n O15 H11 5C8 sing 41 n n C16 H12 5C8 sing 42 n n C17 H13 5C8 sing 43 n n C19 H14 5C8 sing 44 n n C20 H15 5C8 sing 45 n n C22 H16 5C8 sing 46 n n C23 H17 5C8 sing 47 n n C24 H18 5C8 sing 48 n n C25 H19 5C8 sing 49 n n C27 H20 5C8 sing 50 n n # _atom_sites.entry_id 5DKE _atom_sites.fract_transf_matrix[1][1] 0.018954 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00682 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012936 _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] 0.018474 _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 5C8 A 1 601 1 5C8 UNK . F 3 5C8 B 1 601 1 5C8 UNK . G 4 HOH A 1 701 9 HOH HOH . G 4 HOH A 2 702 59 HOH HOH . G 4 HOH A 3 703 24 HOH HOH . G 4 HOH A 4 704 28 HOH HOH . G 4 HOH A 5 705 4 HOH HOH . G 4 HOH A 6 706 46 HOH HOH . G 4 HOH A 7 707 10 HOH HOH . G 4 HOH A 8 708 22 HOH HOH . G 4 HOH A 9 709 21 HOH HOH . G 4 HOH A 10 710 45 HOH HOH . G 4 HOH A 11 711 15 HOH HOH . G 4 HOH A 12 712 16 HOH HOH . G 4 HOH A 13 713 26 HOH HOH . G 4 HOH A 14 714 17 HOH HOH . G 4 HOH A 15 715 3 HOH HOH . G 4 HOH A 16 716 35 HOH HOH . G 4 HOH A 17 717 2 HOH HOH . G 4 HOH A 18 718 12 HOH HOH . G 4 HOH A 19 719 57 HOH HOH . G 4 HOH A 20 720 8 HOH HOH . G 4 HOH A 21 721 39 HOH HOH . G 4 HOH A 22 722 11 HOH HOH . G 4 HOH A 23 723 14 HOH HOH . G 4 HOH A 24 724 1 HOH HOH . G 4 HOH A 25 725 44 HOH HOH . G 4 HOH A 26 726 52 HOH HOH . G 4 HOH A 27 727 36 HOH HOH . G 4 HOH A 28 728 33 HOH HOH . G 4 HOH A 29 729 53 HOH HOH . G 4 HOH A 30 730 47 HOH HOH . H 4 HOH B 1 701 7 HOH HOH . H 4 HOH B 2 702 43 HOH HOH . H 4 HOH B 3 703 41 HOH HOH . H 4 HOH B 4 704 23 HOH HOH . H 4 HOH B 5 705 37 HOH HOH . H 4 HOH B 6 706 58 HOH HOH . H 4 HOH B 7 707 34 HOH HOH . H 4 HOH B 8 708 51 HOH HOH . H 4 HOH B 9 709 38 HOH HOH . H 4 HOH B 10 710 13 HOH HOH . H 4 HOH B 11 711 50 HOH HOH . H 4 HOH B 12 712 18 HOH HOH . H 4 HOH B 13 713 40 HOH HOH . H 4 HOH B 14 714 5 HOH HOH . H 4 HOH B 15 715 19 HOH HOH . H 4 HOH B 16 716 6 HOH HOH . H 4 HOH B 17 717 54 HOH HOH . H 4 HOH B 18 718 42 HOH HOH . H 4 HOH B 19 719 20 HOH HOH . H 4 HOH B 20 720 56 HOH HOH . H 4 HOH B 21 721 25 HOH HOH . H 4 HOH B 22 722 49 HOH HOH . H 4 HOH B 23 723 29 HOH HOH . H 4 HOH B 24 724 55 HOH HOH . H 4 HOH B 25 725 32 HOH HOH . H 4 HOH B 26 726 60 HOH HOH . H 4 HOH B 27 727 30 HOH HOH . I 4 HOH C 1 701 31 HOH HOH . I 4 HOH C 2 702 48 HOH HOH . J 4 HOH D 1 701 27 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 C C01 5C8 . . . F 3 12.734 20.498 33.219 0.78 25.83 ? C01 5C8 601 B 1 HETATM 2 C C02 5C8 . . . F 3 13.274 19.167 33.629 0.78 27.12 ? C02 5C8 601 B 1 HETATM 3 C C03 5C8 . . . F 3 12.632 18.381 34.565 0.78 24.24 ? C03 5C8 601 B 1 HETATM 4 C C04 5C8 . . . F 3 11.214 18.626 34.967 0.78 25.67 ? C04 5C8 601 B 1 HETATM 5 C C05 5C8 . . . F 3 10.189 18.554 34.028 0.78 26.12 ? C05 5C8 601 B 1 HETATM 6 C C06 5C8 . . . F 3 8.878 18.783 34.412 0.78 29.66 ? C06 5C8 601 B 1 HETATM 7 C C07 5C8 . . . F 3 8.58 19.062 35.737 0.78 29.55 ? C07 5C8 601 B 1 HETATM 8 O O08 5C8 . . . F 3 7.274 19.28 36.11 0.78 26.89 ? O08 5C8 601 B 1 HETATM 9 C C09 5C8 . . . F 3 9.597 19.122 36.68 0.78 29.12 ? C09 5C8 601 B 1 HETATM 10 C C10 5C8 . . . F 3 10.911 18.903 36.295 0.78 28.49 ? C10 5C8 601 B 1 HETATM 11 C C11 5C8 . . . F 3 13.29 17.168 35.132 0.78 16.48 ? C11 5C8 601 B 1 HETATM 12 C C12 5C8 . . . F 3 14.348 17.301 36.02 0.78 17.4 ? C12 5C8 601 B 1 HETATM 13 C C13 5C8 . . . F 3 14.962 16.177 36.549 0.78 16.33 ? C13 5C8 601 B 1 HETATM 14 C C14 5C8 . . . F 3 14.518 14.912 36.192 0.78 17.11 ? C14 5C8 601 B 1 HETATM 15 O O15 5C8 . . . F 3 15.126 13.793 36.717 0.78 17.33 ? O15 5C8 601 B 1 HETATM 16 C C16 5C8 . . . F 3 13.459 14.777 35.304 0.78 15.43 ? C16 5C8 601 B 1 HETATM 17 C C17 5C8 . . . F 3 12.846 15.904 34.775 0.78 14.84 ? C17 5C8 601 B 1 HETATM 18 C C18 5C8 . . . F 3 14.642 18.82 33.14 0.78 29.55 ? C18 5C8 601 B 1 HETATM 19 C C19 5C8 . . . F 3 14.875 17.632 32.438 0.78 28.74 ? C19 5C8 601 B 1 HETATM 20 C C20 5C8 . . . F 3 16.159 17.328 31.993 0.78 27.49 ? C20 5C8 601 B 1 HETATM 21 C C21 5C8 . . . F 3 17.232 18.233 32.241 0.78 27.88 ? C21 5C8 601 B 1 HETATM 22 C C22 5C8 . . . F 3 18.546 17.923 31.78 0.78 31.88 ? C22 5C8 601 B 1 HETATM 23 C C23 5C8 . . . F 3 19.597 18.805 32.021 0.78 32.86 ? C23 5C8 601 B 1 HETATM 24 C C24 5C8 . . . F 3 19.363 19.996 32.715 0.78 31.41 ? C24 5C8 601 B 1 HETATM 25 C C25 5C8 . . . F 3 18.078 20.3 33.164 0.78 29.41 ? C25 5C8 601 B 1 HETATM 26 C C26 5C8 . . . F 3 17.004 19.395 32.917 0.78 28.71 ? C26 5C8 601 B 1 HETATM 27 C C27 5C8 . . . F 3 15.69 19.703 33.379 0.78 30.88 ? C27 5C8 601 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #