data_5DYB # _model_server_result.job_id K9InLsMljtRBsB0kjLeh9w _model_server_result.datetime_utc '2024-11-25 13:49:41' _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 5dyb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":900}' # _entry.id 5DYB # _exptl.entry_id 5DYB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 328.404 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "4,4'-(3,4-dihydronaphthalen-2(1H)-ylidenemethanediyl)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 110.16 _cell.angle_gamma 90 _cell.entry_id 5DYB _cell.length_a 54.154 _cell.length_b 81.044 _cell.length_c 58.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYB _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 'C23 H20 O2' _chem_comp.formula_weight 328.404 _chem_comp.id 5K2 _chem_comp.mon_nstd_flag . _chem_comp.name "4,4'-(3,4-dihydronaphthalen-2(1H)-ylidenemethanediyl)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 O02 C21 5K2 sing 1 n n C20 C21 5K2 doub 2 n y C20 C19 5K2 sing 3 n y C21 C22 5K2 sing 4 n y C19 C18 5K2 doub 5 n y C22 C23 5K2 doub 6 n y C18 C23 5K2 sing 7 n y C18 C11 5K2 sing 8 n n C11 C12 5K2 sing 9 n n C11 C10 5K2 doub 10 n n C12 C17 5K2 doub 11 n y C12 C13 5K2 sing 12 n y C17 C16 5K2 sing 13 n y C13 C14 5K2 doub 14 n y C16 C15 5K2 doub 15 n y C14 C15 5K2 sing 16 n y C15 O01 5K2 sing 17 n n C09 C10 5K2 sing 18 n n C09 C08 5K2 sing 19 n n C10 C01 5K2 sing 20 n n C07 C08 5K2 doub 21 n y C07 C06 5K2 sing 22 n y C08 C03 5K2 sing 23 n y C06 C05 5K2 doub 24 n y C01 C02 5K2 sing 25 n n C03 C02 5K2 sing 26 n n C03 C04 5K2 doub 27 n y C05 C04 5K2 sing 28 n y C01 H1 5K2 sing 29 n n C02 H2 5K2 sing 30 n n C02 H3 5K2 sing 31 n n C04 H4 5K2 sing 32 n n C05 H5 5K2 sing 33 n n C06 H6 5K2 sing 34 n n C07 H7 5K2 sing 35 n n C09 H8 5K2 sing 36 n n C09 H9 5K2 sing 37 n n C13 H11 5K2 sing 38 n n C14 H12 5K2 sing 39 n n O01 H13 5K2 sing 40 n n C16 H14 5K2 sing 41 n n C17 H15 5K2 sing 42 n n C19 H16 5K2 sing 43 n n C20 H17 5K2 sing 44 n n O02 H18 5K2 sing 45 n n C22 H19 5K2 sing 46 n n C23 H20 5K2 sing 47 n n C01 H21 5K2 sing 48 n n # _atom_sites.entry_id 5DYB _atom_sites.fract_transf_matrix[1][1] 0.018466 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006779 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012339 _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] 0.018335 _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 5K2 A 1 900 900 5K2 UNK . F 3 5K2 B 1 901 901 5K2 UNK . G 4 HOH A 1 1001 82 HOH HOH . G 4 HOH A 2 1002 77 HOH HOH . G 4 HOH A 3 1003 106 HOH HOH . G 4 HOH A 4 1004 96 HOH HOH . G 4 HOH A 5 1005 19 HOH HOH . G 4 HOH A 6 1006 15 HOH HOH . G 4 HOH A 7 1007 108 HOH HOH . G 4 HOH A 8 1008 69 HOH HOH . G 4 HOH A 9 1009 113 HOH HOH . G 4 HOH A 10 1010 43 HOH HOH . G 4 HOH A 11 1011 28 HOH HOH . G 4 HOH A 12 1012 51 HOH HOH . G 4 HOH A 13 1013 24 HOH HOH . G 4 HOH A 14 1014 34 HOH HOH . G 4 HOH A 15 1015 67 HOH HOH . G 4 HOH A 16 1016 74 HOH HOH . G 4 HOH A 17 1017 66 HOH HOH . G 4 HOH A 18 1018 70 HOH HOH . G 4 HOH A 19 1019 5 HOH HOH . G 4 HOH A 20 1020 35 HOH HOH . G 4 HOH A 21 1021 59 HOH HOH . G 4 HOH A 22 1022 93 HOH HOH . G 4 HOH A 23 1023 16 HOH HOH . G 4 HOH A 24 1024 2 HOH HOH . G 4 HOH A 25 1025 97 HOH HOH . G 4 HOH A 26 1026 22 HOH HOH . G 4 HOH A 27 1027 41 HOH HOH . G 4 HOH A 28 1028 80 HOH HOH . G 4 HOH A 29 1029 12 HOH HOH . G 4 HOH A 30 1030 27 HOH HOH . G 4 HOH A 31 1031 32 HOH HOH . G 4 HOH A 32 1032 20 HOH HOH . G 4 HOH A 33 1033 3 HOH HOH . G 4 HOH A 34 1034 26 HOH HOH . G 4 HOH A 35 1035 52 HOH HOH . G 4 HOH A 36 1036 29 HOH HOH . G 4 HOH A 37 1037 110 HOH HOH . G 4 HOH A 38 1038 116 HOH HOH . G 4 HOH A 39 1039 102 HOH HOH . G 4 HOH A 40 1040 33 HOH HOH . G 4 HOH A 41 1041 86 HOH HOH . G 4 HOH A 42 1042 76 HOH HOH . G 4 HOH A 43 1043 40 HOH HOH . G 4 HOH A 44 1044 88 HOH HOH . G 4 HOH A 45 1045 115 HOH HOH . G 4 HOH A 46 1046 38 HOH HOH . G 4 HOH A 47 1047 54 HOH HOH . G 4 HOH A 48 1048 31 HOH HOH . G 4 HOH A 49 1049 84 HOH HOH . G 4 HOH A 50 1050 50 HOH HOH . G 4 HOH A 51 1051 42 HOH HOH . G 4 HOH A 52 1052 90 HOH HOH . G 4 HOH A 53 1053 120 HOH HOH . G 4 HOH A 54 1054 105 HOH HOH . G 4 HOH A 55 1055 121 HOH HOH . G 4 HOH A 56 1056 55 HOH HOH . G 4 HOH A 57 1057 8 HOH HOH . G 4 HOH A 58 1058 83 HOH HOH . G 4 HOH A 59 1059 61 HOH HOH . G 4 HOH A 60 1060 9 HOH HOH . H 4 HOH B 1 1001 79 HOH HOH . H 4 HOH B 2 1002 65 HOH HOH . H 4 HOH B 3 1003 109 HOH HOH . H 4 HOH B 4 1004 17 HOH HOH . H 4 HOH B 5 1005 75 HOH HOH . H 4 HOH B 6 1006 95 HOH HOH . H 4 HOH B 7 1007 71 HOH HOH . H 4 HOH B 8 1008 7 HOH HOH . H 4 HOH B 9 1009 81 HOH HOH . H 4 HOH B 10 1010 13 HOH HOH . H 4 HOH B 11 1011 6 HOH HOH . H 4 HOH B 12 1012 62 HOH HOH . H 4 HOH B 13 1013 30 HOH HOH . H 4 HOH B 14 1014 4 HOH HOH . H 4 HOH B 15 1015 45 HOH HOH . H 4 HOH B 16 1016 25 HOH HOH . H 4 HOH B 17 1017 117 HOH HOH . H 4 HOH B 18 1018 47 HOH HOH . H 4 HOH B 19 1019 60 HOH HOH . H 4 HOH B 20 1020 107 HOH HOH . H 4 HOH B 21 1021 53 HOH HOH . H 4 HOH B 22 1022 91 HOH HOH . H 4 HOH B 23 1023 21 HOH HOH . H 4 HOH B 24 1024 112 HOH HOH . H 4 HOH B 25 1025 14 HOH HOH . H 4 HOH B 26 1026 94 HOH HOH . H 4 HOH B 27 1027 46 HOH HOH . H 4 HOH B 28 1028 39 HOH HOH . H 4 HOH B 29 1029 1 HOH HOH . H 4 HOH B 30 1030 58 HOH HOH . H 4 HOH B 31 1031 23 HOH HOH . H 4 HOH B 32 1032 72 HOH HOH . H 4 HOH B 33 1033 37 HOH HOH . H 4 HOH B 34 1034 18 HOH HOH . H 4 HOH B 35 1035 118 HOH HOH . H 4 HOH B 36 1036 89 HOH HOH . H 4 HOH B 37 1037 63 HOH HOH . H 4 HOH B 38 1038 56 HOH HOH . H 4 HOH B 39 1039 64 HOH HOH . H 4 HOH B 40 1040 11 HOH HOH . H 4 HOH B 41 1041 57 HOH HOH . H 4 HOH B 42 1042 85 HOH HOH . H 4 HOH B 43 1043 119 HOH HOH . H 4 HOH B 44 1044 49 HOH HOH . H 4 HOH B 45 1045 100 HOH HOH . H 4 HOH B 46 1046 114 HOH HOH . H 4 HOH B 47 1047 101 HOH HOH . H 4 HOH B 48 1048 73 HOH HOH . H 4 HOH B 49 1049 36 HOH HOH . H 4 HOH B 50 1050 99 HOH HOH . H 4 HOH B 51 1051 68 HOH HOH . H 4 HOH B 52 1052 10 HOH HOH . H 4 HOH B 53 1053 104 HOH HOH . H 4 HOH B 54 1054 87 HOH HOH . H 4 HOH B 55 1055 92 HOH HOH . H 4 HOH B 56 1056 48 HOH HOH . H 4 HOH B 57 1057 111 HOH HOH . H 4 HOH B 58 1058 103 HOH HOH . H 4 HOH B 59 1059 78 HOH HOH . H 4 HOH B 60 1060 44 HOH HOH . I 4 HOH C 1 701 98 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 5K2 . . . E 3 19.59 12.571 7.392 1 43 ? C01 5K2 900 A 1 HETATM 2 C C02 5K2 . . . E 3 19.161 11.64 8.549 1 46.87 ? C02 5K2 900 A 1 HETATM 3 C C03 5K2 . . . E 3 18.478 10.492 8.127 1 49.17 ? C03 5K2 900 A 1 HETATM 4 C C04 5K2 . . . E 3 18.438 9.369 8.988 1 53.01 ? C04 5K2 900 A 1 HETATM 5 C C05 5K2 . . . E 3 17.755 8.207 8.594 1 51.96 ? C05 5K2 900 A 1 HETATM 6 C C06 5K2 . . . E 3 17.105 8.161 7.342 1 50.41 ? C06 5K2 900 A 1 HETATM 7 C C07 5K2 . . . E 3 17.135 9.274 6.476 1 48.29 ? C07 5K2 900 A 1 HETATM 8 C C08 5K2 . . . E 3 17.821 10.444 6.863 1 45.25 ? C08 5K2 900 A 1 HETATM 9 C C09 5K2 . . . E 3 17.833 11.54 5.985 1 41.81 ? C09 5K2 900 A 1 HETATM 10 C C10 5K2 . . . E 3 18.837 12.529 6.184 1 37.87 ? C10 5K2 900 A 1 HETATM 11 C C11 5K2 . . . E 3 19.461 13.113 5.043 1 33.72 ? C11 5K2 900 A 1 HETATM 12 C C12 5K2 . . . E 3 20.796 13.541 5.136 1 35.08 ? C12 5K2 900 A 1 HETATM 13 C C13 5K2 . . . E 3 21.842 12.576 5.182 1 39.68 ? C13 5K2 900 A 1 HETATM 14 C C14 5K2 . . . E 3 23.179 12.984 5.268 1 39.89 ? C14 5K2 900 A 1 HETATM 15 C C15 5K2 . . . E 3 23.464 14.37 5.296 1 38.83 ? C15 5K2 900 A 1 HETATM 16 O O01 5K2 . . . E 3 24.767 14.751 5.377 1 39.78 ? O01 5K2 900 A 1 HETATM 17 C C16 5K2 . . . E 3 22.456 15.344 5.244 1 37.88 ? C16 5K2 900 A 1 HETATM 18 C C17 5K2 . . . E 3 21.109 14.93 5.159 1 36.27 ? C17 5K2 900 A 1 HETATM 19 C C18 5K2 . . . E 3 18.755 13.502 3.875 1 31.37 ? C18 5K2 900 A 1 HETATM 20 C C19 5K2 . . . E 3 19.444 13.531 2.642 1 32.15 ? C19 5K2 900 A 1 HETATM 21 C C20 5K2 . . . E 3 18.788 13.926 1.451 1 26.96 ? C20 5K2 900 A 1 HETATM 22 C C21 5K2 . . . E 3 17.43 14.292 1.52 1 29.13 ? C21 5K2 900 A 1 HETATM 23 O O02 5K2 . . . E 3 16.775 14.673 0.393 1 33.67 ? O02 5K2 900 A 1 HETATM 24 C C22 5K2 . . . E 3 16.723 14.27 2.741 1 30.05 ? C22 5K2 900 A 1 HETATM 25 C C23 5K2 . . . E 3 17.388 13.881 3.917 1 31.88 ? C23 5K2 900 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #