data_1XDK # _model_server_result.job_id '_eMC7ptxosgSg8KPrREf9g' _model_server_result.datetime_utc '2024-11-23 16:59:07' _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 1xdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1600}' # _entry.id 1XDK # _exptl.entry_id 1XDK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 300.435 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(9cis)-retinoic acid' _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 1XDK _cell.length_a 115.7 _cell.length_b 115.7 _cell.length_c 247.2 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA octameric 8 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,M,N 1 1 E,F,G,H,K,L,O,P 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 3 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 ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N # _chem_comp.formula 'C20 H28 O2' _chem_comp.formula_weight 300.435 _chem_comp.id 9CR _chem_comp.mon_nstd_flag . _chem_comp.name '(9cis)-retinoic acid' _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 O1 C15 9CR doub 1 n n C15 C14 9CR sing 2 n n C15 O2 9CR sing 3 n n C14 C13 9CR doub 4 e n C13 C12 9CR sing 5 n n C13 C20 9CR sing 6 n n C12 C11 9CR doub 7 e n C11 C10 9CR sing 8 n n C18 C5 9CR sing 9 n n C10 C9 9CR doub 10 z n C9 C19 9CR sing 11 n n C9 C8 9CR sing 12 n n C8 C7 9CR doub 13 e n C5 C4 9CR sing 14 n n C5 C6 9CR doub 15 n n C4 C3 9CR sing 16 n n C7 C6 9CR sing 17 n n C6 C1 9CR sing 18 n n C3 C2 9CR sing 19 n n C1 C17 9CR sing 20 n n C1 C2 9CR sing 21 n n C1 C16 9CR sing 22 n n C2 H1 9CR sing 23 n n C2 H2 9CR sing 24 n n C3 H3 9CR sing 25 n n C3 H4 9CR sing 26 n n C4 H5 9CR sing 27 n n C4 H6 9CR sing 28 n n C7 H7 9CR sing 29 n n C8 H8 9CR sing 30 n n C10 H9 9CR sing 31 n n C11 H10 9CR sing 32 n n C12 H11 9CR sing 33 n n C14 H12 9CR sing 34 n n C16 H13 9CR sing 35 n n C16 H14 9CR sing 36 n n C16 H15 9CR sing 37 n n C17 H16 9CR sing 38 n n C17 H17 9CR sing 39 n n C17 H18 9CR sing 40 n n C18 H19 9CR sing 41 n n C18 H20 9CR sing 42 n n C18 H21 9CR sing 43 n n C19 H22 9CR sing 44 n n C19 H23 9CR sing 45 n n C19 H24 9CR sing 46 n n C20 H25 9CR sing 47 n n C20 H26 9CR sing 48 n n C20 H27 9CR sing 49 n n O2 H28 9CR sing 50 n n # _atom_sites.entry_id 1XDK _atom_sites.fract_transf_matrix[1][1] 0.008643 _atom_sites.fract_transf_matrix[1][2] 0.00499 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00998 _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] 0.004045 _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 I 4 9CR A 1 500 500 9CR REA . J 4 9CR B 1 600 600 9CR REA . K 4 9CR E 1 1500 1500 9CR REA . L 4 9CR F 1 1600 1600 9CR REA . M 5 HOH A 1 701 701 HOH HOH . M 5 HOH A 2 704 704 HOH HOH . M 5 HOH A 3 705 705 HOH HOH . M 5 HOH A 4 706 706 HOH HOH . N 5 HOH B 1 702 702 HOH HOH . N 5 HOH B 2 703 703 HOH HOH . O 5 HOH E 1 707 707 HOH HOH . O 5 HOH E 2 710 710 HOH HOH . O 5 HOH E 3 711 711 HOH HOH . O 5 HOH E 4 712 712 HOH HOH . P 5 HOH F 1 708 708 HOH HOH . P 5 HOH F 2 709 709 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 C1 9CR . . . L 4 36.37 5.061 103.039 1 71.12 ? C1 9CR 1600 F 1 HETATM 2 C C2 9CR . . . L 4 35.078 5.79 102.513 1 70.9 ? C2 9CR 1600 F 1 HETATM 3 C C3 9CR . . . L 4 33.913 4.945 101.986 1 71.56 ? C3 9CR 1600 F 1 HETATM 4 C C4 9CR . . . L 4 33.521 3.829 102.922 1 70.94 ? C4 9CR 1600 F 1 HETATM 5 C C5 9CR . . . L 4 34.666 3.05 103.599 1 71.71 ? C5 9CR 1600 F 1 HETATM 6 C C6 9CR . . . L 4 35.994 3.586 103.67 1 71.61 ? C6 9CR 1600 F 1 HETATM 7 C C7 9CR . . . L 4 37.168 2.895 104.327 1 72.74 ? C7 9CR 1600 F 1 HETATM 8 C C8 9CR . . . L 4 37.613 1.618 104.294 1 72.27 ? C8 9CR 1600 F 1 HETATM 9 C C9 9CR . . . L 4 38.725 0.973 104.911 1 72.9 ? C9 9CR 1600 F 1 HETATM 10 C C10 9CR . . . L 4 38.947 -0.344 104.682 1 73.21 ? C10 9CR 1600 F 1 HETATM 11 C C11 9CR . . . L 4 38.228 -1.345 103.903 1 73.06 ? C11 9CR 1600 F 1 HETATM 12 C C12 9CR . . . L 4 38.628 -2.597 103.738 1 72.46 ? C12 9CR 1600 F 1 HETATM 13 C C13 9CR . . . L 4 37.853 -3.633 102.979 1 73.96 ? C13 9CR 1600 F 1 HETATM 14 C C14 9CR . . . L 4 38.448 -4.795 102.911 1 75.85 ? C14 9CR 1600 F 1 HETATM 15 C C15 9CR . . . L 4 38.173 -6.111 102.316 1 75.87 ? C15 9CR 1600 F 1 HETATM 16 C C16 9CR . . . L 4 36.957 6.083 104.052 1 71.81 ? C16 9CR 1600 F 1 HETATM 17 C C17 9CR . . . L 4 37.368 4.987 101.89 1 69.91 ? C17 9CR 1600 F 1 HETATM 18 C C18 9CR . . . L 4 34.053 1.746 104.094 1 72.15 ? C18 9CR 1600 F 1 HETATM 19 C C19 9CR . . . L 4 39.657 1.768 105.793 1 72.35 ? C19 9CR 1600 F 1 HETATM 20 C C20 9CR . . . L 4 36.513 -3.336 102.356 1 73.62 ? C20 9CR 1600 F 1 HETATM 21 O O1 9CR . . . L 4 37.788 -6.262 101.071 1 77.05 ? O1 9CR 1600 F 1 HETATM 22 O O2 9CR . . . L 4 38.354 -7.095 103.115 1 77.13 ? O2 9CR 1600 F 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #