data_1DIY # _model_server_result.job_id 7E8WotjMGHVxGoia8oINlg _model_server_result.datetime_utc '2024-10-11 00:30:37' _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 1diy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":751}' # _entry.id 1DIY # _exptl.entry_id 1DIY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 292.369 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'octyl beta-D-glucopyranoside' _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 1DIY _cell.length_a 182.1 _cell.length_b 182.1 _cell.length_c 103.64 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DIY _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_644 y+1,x-1,-z-1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 273.15 -157.703226 -34.546667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NDG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 BMA BMA C1 O1 . O6 HO6 . sing 5 ? 3 5 4 MAN BMA C1 O1 . O3 HO3 . sing 6 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG B 661 NAG 2 n B NDG 2 B 2 NDG B 662 NAG 3 n C NAG 1 C 1 NAG C 671 NAG 3 n C NAG 2 C 2 NAG C 672 NAG 3 n C BMA 3 C 3 BMA C 673 BMA 3 n C BMA 4 C 4 BMA C 674 BMA 3 n C MAN 5 C 5 MAN C 675 BMA 4 n D NAG 1 D 1 NAG D 681 NAG 4 n D NAG 2 D 2 NAG D 682 NAG # 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 disulf ? disulf1 A SG CYS 5 A CYS 36 1_555 A SG CYS 16 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 A SG CYS 6 A CYS 37 1_555 A SG CYS 128 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 10 A CYS 41 1_555 A SG CYS 26 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 28 A CYS 59 1_555 A SG CYS 38 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 538 A CYS 569 1_555 A SG CYS 544 A CYS 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 37 A ASN 68 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 113 A ASN 144 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 A ND2 ASN 379 A ASN 410 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NDG . B NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale7 C O6 BMA . C BMA 3 1_555 C C1 BMA . C BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale8 C O3 BMA . C BMA 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? metalc ? metalc1 A NE2 HIS 357 A HIS 388 1_555 I CO COH . A COH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? # _chem_comp.formula 'C14 H28 O6' _chem_comp.formula_weight 292.369 _chem_comp.id BOG _chem_comp.mon_nstd_flag n _chem_comp.name 'octyl beta-D-glucopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'Beta-Octylglucoside;octyl beta-D-glucoside;octyl D-glucoside;octyl 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 O1 BOG sing 147 n n C1 C2 BOG sing 148 n n C1 O5 BOG sing 149 n n C1 H1 BOG sing 150 n n O1 C1' BOG sing 151 n n C2 O2 BOG sing 152 n n C2 C3 BOG sing 153 n n C2 H2 BOG sing 154 n n O2 HO2 BOG sing 155 n n C3 O3 BOG sing 156 n n C3 C4 BOG sing 157 n n C3 H3 BOG sing 158 n n O3 HO3 BOG sing 159 n n C4 O4 BOG sing 160 n n C4 C5 BOG sing 161 n n C4 H4 BOG sing 162 n n O4 HO4 BOG sing 163 n n C5 O5 BOG sing 164 n n C5 C6 BOG sing 165 n n C5 H5 BOG sing 166 n n C6 O6 BOG sing 167 n n C6 H61 BOG sing 168 n n C6 H62 BOG sing 169 n n O6 HO6 BOG sing 170 n n C1' C2' BOG sing 171 n n C1' "H1'1" BOG sing 172 n n C1' "H1'2" BOG sing 173 n n C2' C3' BOG sing 174 n n C2' "H2'1" BOG sing 175 n n C2' "H2'2" BOG sing 176 n n C3' C4' BOG sing 177 n n C3' "H3'1" BOG sing 178 n n C3' "H3'2" BOG sing 179 n n C4' C5' BOG sing 180 n n C4' "H4'1" BOG sing 181 n n C4' "H4'2" BOG sing 182 n n C5' C6' BOG sing 183 n n C5' "H5'1" BOG sing 184 n n C5' "H5'2" BOG sing 185 n n C6' C7' BOG sing 186 n n C6' "H6'1" BOG sing 187 n n C6' "H6'2" BOG sing 188 n n C7' C8' BOG sing 189 n n C7' "H7'1" BOG sing 190 n n C7' "H7'2" BOG sing 191 n n C8' "H8'1" BOG sing 192 n n C8' "H8'2" BOG sing 193 n n C8' "H8'3" BOG sing 194 n n # _pdbx_chem_comp_identifier.comp_id BOG _pdbx_chem_comp_identifier.identifier b-octylglucoside _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 1DIY _atom_sites.fract_transf_matrix[1][1] 0.005491 _atom_sites.fract_transf_matrix[1][2] 0.003171 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006341 _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] 0.009649 _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 5 BOG A 1 750 750 BOG BOG . F 5 BOG A 1 751 751 BOG BOG . G 5 BOG A 1 752 752 BOG BOG . H 5 BOG A 1 753 753 BOG BOG . I 6 COH A 1 601 601 COH COH . J 7 ACD A 1 700 700 ACD ACD . K 8 HOH A 1 800 800 HOH TIP . K 8 HOH A 2 801 801 HOH TIP . K 8 HOH A 3 802 802 HOH TIP . K 8 HOH A 4 803 803 HOH TIP . K 8 HOH A 5 804 804 HOH TIP . K 8 HOH A 6 805 805 HOH TIP . K 8 HOH A 7 806 806 HOH TIP . K 8 HOH A 8 807 807 HOH TIP . K 8 HOH A 9 808 808 HOH TIP . K 8 HOH A 10 809 809 HOH TIP . K 8 HOH A 11 810 810 HOH TIP . K 8 HOH A 12 811 811 HOH TIP . K 8 HOH A 13 812 812 HOH TIP . K 8 HOH A 14 813 813 HOH TIP . K 8 HOH A 15 814 814 HOH TIP . K 8 HOH A 16 815 815 HOH TIP . K 8 HOH A 17 816 816 HOH TIP . K 8 HOH A 18 817 817 HOH TIP . K 8 HOH A 19 818 818 HOH TIP . K 8 HOH A 20 819 819 HOH TIP . K 8 HOH A 21 820 820 HOH TIP . K 8 HOH A 22 821 821 HOH TIP . K 8 HOH A 23 822 822 HOH TIP . K 8 HOH A 24 823 823 HOH TIP . K 8 HOH A 25 824 824 HOH TIP . K 8 HOH A 26 825 825 HOH TIP . K 8 HOH A 27 826 826 HOH TIP . K 8 HOH A 28 827 827 HOH TIP . K 8 HOH A 29 828 828 HOH TIP . K 8 HOH A 30 829 829 HOH TIP . K 8 HOH A 31 830 830 HOH TIP . K 8 HOH A 32 831 831 HOH TIP . K 8 HOH A 33 832 832 HOH TIP . K 8 HOH A 34 833 833 HOH TIP . K 8 HOH A 35 834 834 HOH TIP . K 8 HOH A 36 835 835 HOH TIP . K 8 HOH A 37 836 836 HOH TIP . K 8 HOH A 38 837 837 HOH TIP . K 8 HOH A 39 838 838 HOH TIP . K 8 HOH A 40 839 839 HOH TIP . K 8 HOH A 41 840 840 HOH TIP . K 8 HOH A 42 841 841 HOH TIP . K 8 HOH A 43 842 842 HOH TIP . K 8 HOH A 44 843 843 HOH TIP . K 8 HOH A 45 844 844 HOH TIP . K 8 HOH A 46 845 845 HOH TIP . K 8 HOH A 47 846 846 HOH TIP . K 8 HOH A 48 847 847 HOH TIP . K 8 HOH A 49 848 848 HOH TIP . K 8 HOH A 50 849 849 HOH TIP . K 8 HOH A 51 850 850 HOH TIP . K 8 HOH A 52 851 851 HOH TIP . K 8 HOH A 53 852 852 HOH TIP . K 8 HOH A 54 853 853 HOH TIP . K 8 HOH A 55 854 854 HOH TIP . K 8 HOH A 56 855 855 HOH TIP . K 8 HOH A 57 856 856 HOH TIP . K 8 HOH A 58 857 857 HOH TIP . K 8 HOH A 59 858 858 HOH TIP . K 8 HOH A 60 859 859 HOH TIP . K 8 HOH A 61 860 860 HOH TIP . K 8 HOH A 62 861 861 HOH TIP . K 8 HOH A 63 862 862 HOH TIP . K 8 HOH A 64 863 863 HOH TIP . K 8 HOH A 65 864 864 HOH TIP . K 8 HOH A 66 865 865 HOH TIP . K 8 HOH A 67 866 866 HOH TIP . K 8 HOH A 68 867 867 HOH TIP . K 8 HOH A 69 868 868 HOH TIP . K 8 HOH A 70 869 869 HOH TIP . K 8 HOH A 71 870 870 HOH TIP . K 8 HOH A 72 871 871 HOH TIP . K 8 HOH A 73 872 872 HOH TIP . K 8 HOH A 74 873 873 HOH TIP . K 8 HOH A 75 874 874 HOH TIP . K 8 HOH A 76 875 875 HOH TIP . K 8 HOH A 77 876 876 HOH TIP . K 8 HOH A 78 877 877 HOH TIP . K 8 HOH A 79 878 878 HOH TIP . K 8 HOH A 80 879 879 HOH TIP . K 8 HOH A 81 880 880 HOH TIP . K 8 HOH A 82 881 881 HOH TIP . K 8 HOH A 83 882 882 HOH TIP . K 8 HOH A 84 883 883 HOH TIP . K 8 HOH A 85 884 884 HOH TIP . K 8 HOH A 86 885 885 HOH TIP . K 8 HOH A 87 886 886 HOH TIP . K 8 HOH A 88 887 887 HOH TIP . K 8 HOH A 89 888 888 HOH TIP . K 8 HOH A 90 889 889 HOH TIP . K 8 HOH A 91 890 890 HOH TIP . K 8 HOH A 92 891 891 HOH TIP . K 8 HOH A 93 892 892 HOH TIP . K 8 HOH A 94 893 893 HOH TIP . K 8 HOH A 95 894 894 HOH TIP . K 8 HOH A 96 895 895 HOH TIP . K 8 HOH A 97 896 896 HOH TIP . K 8 HOH A 98 897 897 HOH TIP . K 8 HOH A 99 898 898 HOH TIP . K 8 HOH A 100 899 899 HOH TIP . K 8 HOH A 101 900 900 HOH TIP . K 8 HOH A 102 901 901 HOH TIP . K 8 HOH A 103 902 902 HOH TIP . K 8 HOH A 104 903 903 HOH TIP . K 8 HOH A 105 904 904 HOH TIP . K 8 HOH A 106 905 905 HOH TIP . K 8 HOH A 107 906 906 HOH TIP . K 8 HOH A 108 907 907 HOH TIP . K 8 HOH A 109 908 908 HOH TIP . # 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 BOG . . . F 5 250.102 118.125 -37.705 1 64.9 ? C1 BOG 751 A 1 HETATM 2 O O1 BOG . . . F 5 251.261 117.457 -38.091 1 64.9 ? O1 BOG 751 A 1 HETATM 3 C C2 BOG . . . F 5 249.068 118.04 -38.818 1 64.9 ? C2 BOG 751 A 1 HETATM 4 O O2 BOG . . . F 5 249.631 118.528 -40.029 1 64.9 ? O2 BOG 751 A 1 HETATM 5 C C3 BOG . . . F 5 247.829 118.863 -38.409 1 64.9 ? C3 BOG 751 A 1 HETATM 6 O O3 BOG . . . F 5 246.8 118.729 -39.395 1 64.9 ? O3 BOG 751 A 1 HETATM 7 C C4 BOG . . . F 5 247.305 118.363 -37.046 1 64.9 ? C4 BOG 751 A 1 HETATM 8 O O4 BOG . . . F 5 246.301 119.244 -36.548 1 64.9 ? O4 BOG 751 A 1 HETATM 9 C C5 BOG . . . F 5 248.422 118.22 -35.986 1 64.9 ? C5 BOG 751 A 1 HETATM 10 O O5 BOG . . . F 5 249.574 117.517 -36.52 1 64.9 ? O5 BOG 751 A 1 HETATM 11 C C6 BOG . . . F 5 247.919 117.393 -34.808 1 64.9 ? C6 BOG 751 A 1 HETATM 12 O O6 BOG . . . F 5 247.033 116.354 -35.231 1 64.9 ? O6 BOG 751 A 1 HETATM 13 C C1' BOG . . . F 5 251.897 116.591 -37.123 1 64.9 ? C1' BOG 751 A 1 HETATM 14 C C2' BOG . . . F 5 253.411 116.647 -37.283 1 64.9 ? C2' BOG 751 A 1 HETATM 15 C C3' BOG . . . F 5 254.019 117.854 -36.551 1 64.9 ? C3' BOG 751 A 1 HETATM 16 C C4' BOG . . . F 5 255.207 118.412 -37.34 1 64.9 ? C4' BOG 751 A 1 HETATM 17 C C5' BOG . . . F 5 256.064 119.336 -36.505 1 64.9 ? C5' BOG 751 A 1 HETATM 18 C C6' BOG . . . F 5 257.045 120.087 -37.385 1 64.9 ? C6' BOG 751 A 1 HETATM 19 C C7' BOG . . . F 5 257.781 119.157 -38.328 1 64.9 ? C7' BOG 751 A 1 HETATM 20 C C8' BOG . . . F 5 258.776 119.925 -39.163 1 64.9 ? C8' BOG 751 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #