data_1XME # _model_server_result.job_id SPacfLuiJCourNz9bZ90JQ _model_server_result.datetime_utc '2025-07-04 04:42:51' _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 1xme # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":805}' # _entry.id 1XME # _exptl.entry_id 1XME _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.395 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'nonyl beta-D-glucopyranoside' _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 1XME _cell.length_a 114.902 _cell.length_b 114.902 _cell.length_c 177.064 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XME _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A NE2 HIS 239 A HIS 233 1_555 A CE2 TYR 243 A TYR 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? metalc ? metalc1 A NE2 HIS 78 A HIS 72 1_555 F FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc2 A ND1 HIS 239 A HIS 233 1_555 E CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc3 A NE2 HIS 288 A HIS 282 1_555 E CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc4 A NE2 HIS 289 A HIS 283 1_555 E CU CU . A CU 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc5 A NE2 HIS 390 A HIS 384 1_555 G FE HAS . A HAS 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc6 A NE2 HIS 392 A HIS 386 1_555 F FE HEM . A HEM 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc7 G FE HAS . A HAS 801 1_555 J O HOH . A HOH 867 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc8 E CU CU . A CU 803 1_555 J O HOH . A HOH 867 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc9 B ND1 HIS 114 B HIS 114 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc10 B SG CYS 149 B CYS 149 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc11 B SG CYS 149 B CYS 149 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc12 B O GLN 151 B GLN 151 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc13 B SG CYS 153 B CYS 153 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc14 B SG CYS 153 B CYS 153 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc15 B ND1 HIS 157 B HIS 157 1_555 I CU1 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc16 B SD MET 160 B MET 160 1_555 I CU2 CUA . B CUA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? # _chem_comp.formula 'C15 H30 O6' _chem_comp.formula_weight 306.395 _chem_comp.id BNG _chem_comp.mon_nstd_flag n _chem_comp.name 'nonyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Beta-NONYLGLUCOSIDE;nonyl beta-D-glucoside;nonyl D-glucoside;nonyl glucoside' # 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 C1 C2 BNG sing 70 n n C1 O1 BNG sing 71 n n C1 O5 BNG sing 72 n n C1 H1 BNG sing 73 n n C2 C3 BNG sing 74 n n C2 O2 BNG sing 75 n n C2 H2 BNG sing 76 n n C3 C4 BNG sing 77 n n C3 O3 BNG sing 78 n n C3 H3 BNG sing 79 n n C4 C5 BNG sing 80 n n C4 O4 BNG sing 81 n n C4 H4 BNG sing 82 n n C5 C6 BNG sing 83 n n C5 O5 BNG sing 84 n n C5 H5 BNG sing 85 n n C6 O6 BNG sing 86 n n C6 H61 BNG sing 87 n n C6 H62 BNG sing 88 n n C1' C2' BNG sing 89 n n C1' O1 BNG sing 90 n n C1' "H1'1" BNG sing 91 n n C1' "H1'2" BNG sing 92 n n C2' C3' BNG sing 93 n n C2' "H2'1" BNG sing 94 n n C2' "H2'2" BNG sing 95 n n C3' C4' BNG sing 96 n n C3' "H3'1" BNG sing 97 n n C3' "H3'2" BNG sing 98 n n C4' C5' BNG sing 99 n n C4' "H4'1" BNG sing 100 n n C4' "H4'2" BNG sing 101 n n C5' C6' BNG sing 102 n n C5' "H5'1" BNG sing 103 n n C5' "H5'2" BNG sing 104 n n C6' C7' BNG sing 105 n n C6' "H6'1" BNG sing 106 n n C6' "H6'2" BNG sing 107 n n C7' C8' BNG sing 108 n n C7' "H7'1" BNG sing 109 n n C7' "H7'2" BNG sing 110 n n C8' C9' BNG sing 111 n n C8' "H8'1" BNG sing 112 n n C8' "H8'2" BNG sing 113 n n C9' "H9'1" BNG sing 114 n n C9' "H9'2" BNG sing 115 n n C9' "H9'3" BNG sing 116 n n O2 HO2 BNG sing 117 n n O3 HO3 BNG sing 118 n n O4 HO4 BNG sing 119 n n O6 HO6 BNG sing 120 n n # _pdbx_chem_comp_identifier.comp_id BNG _pdbx_chem_comp_identifier.identifier b-nonylglucoside _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 1XME _atom_sites.fract_transf_matrix[1][1] 0.008703 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008703 _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] 0.005648 _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 D 4 BNG A 1 805 805 BNG BNG . E 5 CU A 1 803 803 CU 1CU . F 6 HEM A 1 800 800 HEM HEM . G 7 HAS A 1 801 801 HAS HAS . H 8 GOL A 1 804 804 GOL GOL . I 9 CUA B 1 802 802 CUA CUA . J 10 HOH A 1 806 1 HOH HOH . J 10 HOH A 2 807 2 HOH HOH . J 10 HOH A 3 808 3 HOH HOH . J 10 HOH A 4 809 4 HOH HOH . J 10 HOH A 5 810 5 HOH HOH . J 10 HOH A 6 811 6 HOH HOH . J 10 HOH A 7 812 7 HOH HOH . J 10 HOH A 8 813 9 HOH HOH . J 10 HOH A 9 814 10 HOH HOH . J 10 HOH A 10 815 11 HOH HOH . J 10 HOH A 11 816 13 HOH HOH . J 10 HOH A 12 817 14 HOH HOH . J 10 HOH A 13 818 15 HOH HOH . J 10 HOH A 14 819 16 HOH HOH . J 10 HOH A 15 820 18 HOH HOH . J 10 HOH A 16 821 19 HOH HOH . J 10 HOH A 17 822 20 HOH HOH . J 10 HOH A 18 823 21 HOH HOH . J 10 HOH A 19 824 23 HOH HOH . J 10 HOH A 20 825 24 HOH HOH . J 10 HOH A 21 826 25 HOH HOH . J 10 HOH A 22 827 26 HOH HOH . J 10 HOH A 23 828 27 HOH HOH . J 10 HOH A 24 829 29 HOH HOH . J 10 HOH A 25 830 30 HOH HOH . J 10 HOH A 26 831 31 HOH HOH . J 10 HOH A 27 832 32 HOH HOH . J 10 HOH A 28 833 33 HOH HOH . J 10 HOH A 29 834 34 HOH HOH . J 10 HOH A 30 835 37 HOH HOH . J 10 HOH A 31 836 38 HOH HOH . J 10 HOH A 32 837 39 HOH HOH . J 10 HOH A 33 838 40 HOH HOH . J 10 HOH A 34 839 41 HOH HOH . J 10 HOH A 35 840 44 HOH HOH . J 10 HOH A 36 841 45 HOH HOH . J 10 HOH A 37 842 46 HOH HOH . J 10 HOH A 38 843 47 HOH HOH . J 10 HOH A 39 844 48 HOH HOH . J 10 HOH A 40 845 50 HOH HOH . J 10 HOH A 41 846 52 HOH HOH . J 10 HOH A 42 847 53 HOH HOH . J 10 HOH A 43 848 54 HOH HOH . J 10 HOH A 44 849 55 HOH HOH . J 10 HOH A 45 850 56 HOH HOH . J 10 HOH A 46 851 59 HOH HOH . J 10 HOH A 47 852 60 HOH HOH . J 10 HOH A 48 853 61 HOH HOH . J 10 HOH A 49 854 63 HOH HOH . J 10 HOH A 50 855 64 HOH HOH . J 10 HOH A 51 856 66 HOH HOH . J 10 HOH A 52 857 67 HOH HOH . J 10 HOH A 53 858 68 HOH HOH . J 10 HOH A 54 859 69 HOH HOH . J 10 HOH A 55 860 71 HOH HOH . J 10 HOH A 56 861 72 HOH HOH . J 10 HOH A 57 862 73 HOH HOH . J 10 HOH A 58 863 74 HOH HOH . J 10 HOH A 59 864 75 HOH HOH . J 10 HOH A 60 865 76 HOH HOH . J 10 HOH A 61 866 77 HOH HOH . J 10 HOH A 62 867 803 HOH 1CU . K 10 HOH B 1 803 12 HOH HOH . K 10 HOH B 2 804 17 HOH HOH . K 10 HOH B 3 805 22 HOH HOH . K 10 HOH B 4 806 28 HOH HOH . K 10 HOH B 5 807 35 HOH HOH . K 10 HOH B 6 808 36 HOH HOH . K 10 HOH B 7 809 42 HOH HOH . K 10 HOH B 8 810 43 HOH HOH . K 10 HOH B 9 811 49 HOH HOH . K 10 HOH B 10 812 51 HOH HOH . K 10 HOH B 11 813 57 HOH HOH . K 10 HOH B 12 814 58 HOH HOH . K 10 HOH B 13 815 62 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 BNG . . . D 4 72.696 47.921 31.182 1 62.57 ? C1 BNG 805 A 1 HETATM 2 C C2 BNG . . . D 4 71.726 49.086 31.627 1 62.28 ? C2 BNG 805 A 1 HETATM 3 C C3 BNG . . . D 4 71.531 50.058 30.416 1 62.29 ? C3 BNG 805 A 1 HETATM 4 C C4 BNG . . . D 4 72.907 50.657 30.113 1 62.34 ? C4 BNG 805 A 1 HETATM 5 C C5 BNG . . . D 4 73.867 49.464 29.686 1 61.32 ? C5 BNG 805 A 1 HETATM 6 C C6 BNG . . . D 4 75.252 49.995 29.381 1 61.09 ? C6 BNG 805 A 1 HETATM 7 C C1' BNG . . . D 4 71.764 46.055 32.441 1 65.76 ? C1' BNG 805 A 1 HETATM 8 C C2' BNG . . . D 4 71.95 45.061 33.65 1 65.76 ? C2' BNG 805 A 1 HETATM 9 C C3' BNG . . . D 4 73.221 44.557 33.559 1 64.83 ? C3' BNG 805 A 1 HETATM 10 C C4' BNG . . . D 4 73.156 43.087 33.802 1 64.66 ? C4' BNG 805 A 1 HETATM 11 C C5' BNG . . . D 4 74.572 42.516 33.689 1 63.93 ? C5' BNG 805 A 1 HETATM 12 C C6' BNG . . . D 4 74.601 41.014 33.921 1 62.13 ? C6' BNG 805 A 1 HETATM 13 C C7' BNG . . . D 4 76.061 40.531 33.735 1 61.13 ? C7' BNG 805 A 1 HETATM 14 C C8' BNG . . . D 4 76.208 39.016 33.916 1 59.82 ? C8' BNG 805 A 1 HETATM 15 C C9' BNG . . . D 4 77.67 38.604 33.673 1 59.52 ? C9' BNG 805 A 1 HETATM 16 O O1 BNG . . . D 4 72.899 47.012 32.295 1 64.06 ? O1 BNG 805 A 1 HETATM 17 O O2 BNG . . . D 4 70.444 48.517 31.992 1 62.65 ? O2 BNG 805 A 1 HETATM 18 O O3 BNG . . . D 4 70.632 51.14 30.778 1 60.54 ? O3 BNG 805 A 1 HETATM 19 O O4 BNG . . . D 4 72.761 51.623 29.015 1 64.56 ? O4 BNG 805 A 1 HETATM 20 O O5 BNG . . . D 4 74 48.509 30.782 1 60.69 ? O5 BNG 805 A 1 HETATM 21 O O6 BNG . . . D 4 76.107 48.887 29.052 1 63.67 ? O6 BNG 805 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #