data_1KU6 # _model_server_result.job_id 2vUp3HFPvDp1yaOV5XlB_Q _model_server_result.datetime_utc '2024-11-26 17:13:49' _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 1ku6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1509}' # _entry.id 1KU6 # _exptl.entry_id 1KU6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 120 _cell.entry_id 1KU6 _cell.length_a 73.8 _cell.length_b 73.8 _cell.length_c 548.62 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KU6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1 A,B,C,D,E,F 2 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' 10_665 -y+1,-x+1,-z+1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 36.9 63.912675 91.436667 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 69 A CYS 69 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 257 A CYS 257 1_555 A SG CYS 272 A CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 409 A CYS 409 1_555 A SG CYS 529 A CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 B SG CYS 3 B CYS 3 1_555 B SG CYS 22 B CYS 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf5 B SG CYS 17 B CYS 17 1_555 B SG CYS 39 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 B SG CYS 41 B CYS 41 1_555 B SG CYS 52 B CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 B SG CYS 53 B CYS 53 1_555 B SG CYS 59 B CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 350 A ASN 350 1_555 C C1 NAG . A NAG 1509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 246 n n C1 O1 NAG sing 247 n n C1 O5 NAG sing 248 n n C1 H1 NAG sing 249 n n C2 C3 NAG sing 250 n n C2 N2 NAG sing 251 n n C2 H2 NAG sing 252 n n C3 C4 NAG sing 253 n n C3 O3 NAG sing 254 n n C3 H3 NAG sing 255 n n C4 C5 NAG sing 256 n n C4 O4 NAG sing 257 n n C4 H4 NAG sing 258 n n C5 C6 NAG sing 259 n n C5 O5 NAG sing 260 n n C5 H5 NAG sing 261 n n C6 O6 NAG sing 262 n n C6 H61 NAG sing 263 n n C6 H62 NAG sing 264 n n C7 C8 NAG sing 265 n n C7 N2 NAG sing 266 n n C7 O7 NAG doub 267 n n C8 H81 NAG sing 268 n n C8 H82 NAG sing 269 n n C8 H83 NAG sing 270 n n N2 HN2 NAG sing 271 n n O1 HO1 NAG sing 272 n n O3 HO3 NAG sing 273 n n O4 HO4 NAG sing 274 n n O6 HO6 NAG sing 275 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 1KU6 _atom_sites.fract_transf_matrix[1][1] 0.01355 _atom_sites.fract_transf_matrix[1][2] 0.007823 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015646 _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] 0.001823 _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 C 3 NAG A 1 1509 509 NAG NAG . D 4 EDO A 1 701 701 EDO EDO . E 5 HOH A 1 702 702 HOH WAT . E 5 HOH A 2 703 703 HOH WAT . E 5 HOH A 3 704 704 HOH WAT . E 5 HOH A 4 705 705 HOH WAT . E 5 HOH A 5 706 706 HOH WAT . E 5 HOH A 6 707 707 HOH WAT . E 5 HOH A 7 709 709 HOH WAT . E 5 HOH A 8 710 710 HOH WAT . E 5 HOH A 9 711 711 HOH WAT . E 5 HOH A 10 712 712 HOH WAT . E 5 HOH A 11 713 713 HOH WAT . E 5 HOH A 12 714 714 HOH WAT . E 5 HOH A 13 715 715 HOH WAT . E 5 HOH A 14 716 716 HOH WAT . E 5 HOH A 15 717 717 HOH WAT . E 5 HOH A 16 718 718 HOH WAT . E 5 HOH A 17 719 719 HOH WAT . E 5 HOH A 18 720 720 HOH WAT . E 5 HOH A 19 721 721 HOH WAT . E 5 HOH A 20 722 722 HOH WAT . E 5 HOH A 21 723 723 HOH WAT . E 5 HOH A 22 724 724 HOH WAT . E 5 HOH A 23 725 725 HOH WAT . E 5 HOH A 24 726 726 HOH WAT . E 5 HOH A 25 727 727 HOH WAT . E 5 HOH A 26 731 731 HOH WAT . E 5 HOH A 27 732 732 HOH WAT . E 5 HOH A 28 733 733 HOH WAT . E 5 HOH A 29 734 734 HOH WAT . E 5 HOH A 30 735 735 HOH WAT . E 5 HOH A 31 736 736 HOH WAT . E 5 HOH A 32 737 737 HOH WAT . E 5 HOH A 33 738 738 HOH WAT . E 5 HOH A 34 739 739 HOH WAT . E 5 HOH A 35 740 740 HOH WAT . E 5 HOH A 36 741 741 HOH WAT . E 5 HOH A 37 742 742 HOH WAT . E 5 HOH A 38 743 743 HOH WAT . E 5 HOH A 39 744 744 HOH WAT . E 5 HOH A 40 745 745 HOH WAT . E 5 HOH A 41 746 746 HOH WAT . E 5 HOH A 42 747 747 HOH WAT . E 5 HOH A 43 748 748 HOH WAT . E 5 HOH A 44 749 749 HOH WAT . E 5 HOH A 45 750 750 HOH WAT . E 5 HOH A 46 751 751 HOH WAT . E 5 HOH A 47 752 752 HOH WAT . E 5 HOH A 48 753 753 HOH WAT . E 5 HOH A 49 754 754 HOH WAT . E 5 HOH A 50 755 755 HOH WAT . E 5 HOH A 51 756 756 HOH WAT . E 5 HOH A 52 757 757 HOH WAT . E 5 HOH A 53 758 758 HOH WAT . E 5 HOH A 54 759 759 HOH WAT . E 5 HOH A 55 760 760 HOH WAT . E 5 HOH A 56 761 761 HOH WAT . E 5 HOH A 57 763 763 HOH WAT . E 5 HOH A 58 764 764 HOH WAT . E 5 HOH A 59 765 765 HOH WAT . E 5 HOH A 60 767 767 HOH WAT . E 5 HOH A 61 768 768 HOH WAT . E 5 HOH A 62 769 769 HOH WAT . E 5 HOH A 63 770 770 HOH WAT . E 5 HOH A 64 772 772 HOH WAT . E 5 HOH A 65 774 774 HOH WAT . E 5 HOH A 66 775 775 HOH WAT . E 5 HOH A 67 776 776 HOH WAT . E 5 HOH A 68 777 777 HOH WAT . E 5 HOH A 69 779 779 HOH WAT . E 5 HOH A 70 780 780 HOH WAT . E 5 HOH A 71 781 781 HOH WAT . E 5 HOH A 72 782 782 HOH WAT . E 5 HOH A 73 784 784 HOH WAT . E 5 HOH A 74 785 785 HOH WAT . E 5 HOH A 75 786 786 HOH WAT . E 5 HOH A 76 788 788 HOH WAT . E 5 HOH A 77 789 789 HOH WAT . E 5 HOH A 78 790 790 HOH WAT . E 5 HOH A 79 791 791 HOH WAT . E 5 HOH A 80 792 792 HOH WAT . E 5 HOH A 81 793 793 HOH WAT . E 5 HOH A 82 794 794 HOH WAT . E 5 HOH A 83 795 795 HOH WAT . E 5 HOH A 84 796 796 HOH WAT . E 5 HOH A 85 797 797 HOH WAT . E 5 HOH A 86 798 798 HOH WAT . E 5 HOH A 87 799 799 HOH WAT . E 5 HOH A 88 800 800 HOH WAT . E 5 HOH A 89 801 801 HOH WAT . E 5 HOH A 90 802 802 HOH WAT . E 5 HOH A 91 803 803 HOH WAT . E 5 HOH A 92 804 804 HOH WAT . E 5 HOH A 93 805 805 HOH WAT . E 5 HOH A 94 806 806 HOH WAT . E 5 HOH A 95 808 808 HOH WAT . E 5 HOH A 96 809 809 HOH WAT . E 5 HOH A 97 810 810 HOH WAT . E 5 HOH A 98 811 811 HOH WAT . E 5 HOH A 99 813 813 HOH WAT . E 5 HOH A 100 814 814 HOH WAT . E 5 HOH A 101 815 815 HOH WAT . E 5 HOH A 102 816 816 HOH WAT . E 5 HOH A 103 817 817 HOH WAT . E 5 HOH A 104 819 819 HOH WAT . E 5 HOH A 105 820 820 HOH WAT . E 5 HOH A 106 821 821 HOH WAT . E 5 HOH A 107 822 822 HOH WAT . E 5 HOH A 108 824 824 HOH WAT . E 5 HOH A 109 825 825 HOH WAT . E 5 HOH A 110 826 826 HOH WAT . E 5 HOH A 111 827 827 HOH WAT . E 5 HOH A 112 828 828 HOH WAT . E 5 HOH A 113 829 829 HOH WAT . E 5 HOH A 114 830 830 HOH WAT . E 5 HOH A 115 831 831 HOH WAT . E 5 HOH A 116 832 832 HOH WAT . E 5 HOH A 117 833 833 HOH WAT . E 5 HOH A 118 834 834 HOH WAT . E 5 HOH A 119 835 835 HOH WAT . E 5 HOH A 120 836 836 HOH WAT . E 5 HOH A 121 837 837 HOH WAT . E 5 HOH A 122 838 838 HOH WAT . E 5 HOH A 123 839 839 HOH WAT . E 5 HOH A 124 840 840 HOH WAT . E 5 HOH A 125 841 841 HOH WAT . E 5 HOH A 126 842 842 HOH WAT . E 5 HOH A 127 843 843 HOH WAT . E 5 HOH A 128 844 844 HOH WAT . E 5 HOH A 129 845 845 HOH WAT . E 5 HOH A 130 847 847 HOH WAT . E 5 HOH A 131 848 848 HOH WAT . E 5 HOH A 132 851 851 HOH WAT . E 5 HOH A 133 852 852 HOH WAT . E 5 HOH A 134 853 853 HOH WAT . E 5 HOH A 135 854 854 HOH WAT . E 5 HOH A 136 855 855 HOH WAT . E 5 HOH A 137 857 857 HOH WAT . E 5 HOH A 138 859 859 HOH WAT . E 5 HOH A 139 860 860 HOH WAT . E 5 HOH A 140 861 861 HOH WAT . E 5 HOH A 141 862 862 HOH WAT . E 5 HOH A 142 863 863 HOH WAT . E 5 HOH A 143 864 864 HOH WAT . E 5 HOH A 144 865 865 HOH WAT . E 5 HOH A 145 867 867 HOH WAT . E 5 HOH A 146 869 869 HOH WAT . E 5 HOH A 147 870 870 HOH WAT . E 5 HOH A 148 871 871 HOH WAT . E 5 HOH A 149 872 872 HOH WAT . E 5 HOH A 150 874 874 HOH WAT . E 5 HOH A 151 875 875 HOH WAT . E 5 HOH A 152 876 876 HOH WAT . E 5 HOH A 153 877 877 HOH WAT . E 5 HOH A 154 878 878 HOH WAT . E 5 HOH A 155 879 879 HOH WAT . E 5 HOH A 156 880 880 HOH WAT . E 5 HOH A 157 881 881 HOH WAT . E 5 HOH A 158 882 882 HOH WAT . E 5 HOH A 159 883 883 HOH WAT . E 5 HOH A 160 885 885 HOH WAT . E 5 HOH A 161 886 886 HOH WAT . E 5 HOH A 162 887 887 HOH WAT . E 5 HOH A 163 888 888 HOH WAT . E 5 HOH A 164 889 889 HOH WAT . E 5 HOH A 165 890 890 HOH WAT . E 5 HOH A 166 891 891 HOH WAT . F 5 HOH B 1 708 708 HOH WAT . F 5 HOH B 2 728 728 HOH WAT . F 5 HOH B 3 729 729 HOH WAT . F 5 HOH B 4 730 730 HOH WAT . F 5 HOH B 5 762 762 HOH WAT . F 5 HOH B 6 766 766 HOH WAT . F 5 HOH B 7 771 771 HOH WAT . F 5 HOH B 8 773 773 HOH WAT . F 5 HOH B 9 778 778 HOH WAT . F 5 HOH B 10 783 783 HOH WAT . F 5 HOH B 11 787 787 HOH WAT . F 5 HOH B 12 807 807 HOH WAT . F 5 HOH B 13 812 812 HOH WAT . F 5 HOH B 14 818 818 HOH WAT . F 5 HOH B 15 823 823 HOH WAT . F 5 HOH B 16 846 846 HOH WAT . F 5 HOH B 17 849 849 HOH WAT . F 5 HOH B 18 850 850 HOH WAT . F 5 HOH B 19 856 856 HOH WAT . F 5 HOH B 20 858 858 HOH WAT . F 5 HOH B 21 866 866 HOH WAT . F 5 HOH B 22 868 868 HOH WAT . F 5 HOH B 23 873 873 HOH WAT . F 5 HOH B 24 884 884 HOH WAT . # 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 NAG . . . C 3 19.91 62.05 31.412 1 84.65 ? C1 NAG 1509 A 1 HETATM 2 C C2 NAG . . . C 3 19.885 62.803 32.749 1 86.05 ? C2 NAG 1509 A 1 HETATM 3 C C3 NAG . . . C 3 18.475 63.348 33.009 1 87.41 ? C3 NAG 1509 A 1 HETATM 4 C C4 NAG . . . C 3 18.034 64.256 31.834 1 87.41 ? C4 NAG 1509 A 1 HETATM 5 C C5 NAG . . . C 3 18.236 63.552 30.46 1 86.76 ? C5 NAG 1509 A 1 HETATM 6 C C6 NAG . . . C 3 18.105 64.531 29.28 1 87.16 ? C6 NAG 1509 A 1 HETATM 7 C C7 NAG . . . C 3 21.484 62.144 34.436 1 87.74 ? C7 NAG 1509 A 1 HETATM 8 C C8 NAG . . . C 3 22.474 60.974 34.401 1 86.84 ? C8 NAG 1509 A 1 HETATM 9 N N2 NAG . . . C 3 20.306 61.943 33.841 1 87.38 ? N2 NAG 1509 A 1 HETATM 10 O O3 NAG . . . C 3 18.451 64.081 34.242 1 86.13 ? O3 NAG 1509 A 1 HETATM 11 O O4 NAG . . . C 3 16.657 64.616 31.999 1 87.26 ? O4 NAG 1509 A 1 HETATM 12 O O5 NAG . . . C 3 19.563 62.961 30.351 1 86.77 ? O5 NAG 1509 A 1 HETATM 13 O O6 NAG . . . C 3 19.338 64.699 28.567 1 84.28 ? O6 NAG 1509 A 1 HETATM 14 O O7 NAG . . . C 3 21.793 63.217 34.994 1 86.73 ? O7 NAG 1509 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #