data_6IDB # _model_server_result.job_id '_tMvru1ofc6DQw-HlvsQvw' _model_server_result.datetime_utc '2024-10-17 12:21:34' _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 6idb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":804}' # _entry.id 6IDB # _exptl.entry_id 6IDB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 90 _cell.angle_gamma 120 _cell.entry_id 6IDB _cell.length_a 115.956 _cell.length_b 115.956 _cell.length_c 297.05 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 2 1 GAL NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 SIA GAL C2 O2 . O6 HO6 . 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 3 n C NAG 1 C 1 NAG A 803 NAG 3 n C GAL 2 C 2 GAL A 802 GAL 3 n C SIA 3 C 3 SIA A 801 SIA # 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 4 A CYS 4 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 42 A CYS 42 1_555 A SG CYS 268 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? disulf ? disulf3 A SG CYS 54 A CYS 54 1_555 A SG CYS 66 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? disulf ? disulf4 A SG CYS 87 A CYS 87 1_555 A SG CYS 129 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf5 A SG CYS 272 A CYS 272 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 28 A ASN 28 1_555 D C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale2 B ND2 ASN 82 B ASN 82 1_555 E C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 C O6 GAL . C GAL 2 1_555 C C2 SIA . C SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 6IDB _atom_sites.fract_transf_matrix[1][1] 0.008624 _atom_sites.fract_transf_matrix[1][2] 0.004979 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009958 _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] 0.003366 _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 NAG A 1 804 489 NAG NAG . E 4 NAG B 1 201 510 NAG NAG . F 5 HOH A 1 901 91 HOH HOH . F 5 HOH A 2 902 97 HOH HOH . F 5 HOH A 3 903 65 HOH HOH . F 5 HOH A 4 904 38 HOH HOH . F 5 HOH A 5 905 83 HOH HOH . F 5 HOH A 6 906 51 HOH HOH . F 5 HOH A 7 907 16 HOH HOH . F 5 HOH A 8 908 34 HOH HOH . F 5 HOH A 9 909 5 HOH HOH . F 5 HOH A 10 910 62 HOH HOH . F 5 HOH A 11 911 132 HOH HOH . F 5 HOH A 12 912 94 HOH HOH . F 5 HOH A 13 913 150 HOH HOH . F 5 HOH A 14 914 59 HOH HOH . F 5 HOH A 15 915 99 HOH HOH . F 5 HOH A 16 916 23 HOH HOH . F 5 HOH A 17 917 47 HOH HOH . F 5 HOH A 18 918 4 HOH HOH . F 5 HOH A 19 919 41 HOH HOH . F 5 HOH A 20 920 55 HOH HOH . F 5 HOH A 21 921 9 HOH HOH . F 5 HOH A 22 922 24 HOH HOH . F 5 HOH A 23 923 31 HOH HOH . F 5 HOH A 24 924 135 HOH HOH . F 5 HOH A 25 925 53 HOH HOH . F 5 HOH A 26 926 118 HOH HOH . F 5 HOH A 27 927 61 HOH HOH . F 5 HOH A 28 928 21 HOH HOH . F 5 HOH A 29 929 117 HOH HOH . F 5 HOH A 30 930 78 HOH HOH . F 5 HOH A 31 931 42 HOH HOH . F 5 HOH A 32 932 114 HOH HOH . F 5 HOH A 33 933 40 HOH HOH . F 5 HOH A 34 934 12 HOH HOH . F 5 HOH A 35 935 7 HOH HOH . F 5 HOH A 36 936 33 HOH HOH . F 5 HOH A 37 937 8 HOH HOH . F 5 HOH A 38 938 20 HOH HOH . F 5 HOH A 39 939 136 HOH HOH . F 5 HOH A 40 940 127 HOH HOH . F 5 HOH A 41 941 66 HOH HOH . F 5 HOH A 42 942 126 HOH HOH . F 5 HOH A 43 943 2 HOH HOH . F 5 HOH A 44 944 156 HOH HOH . F 5 HOH A 45 945 39 HOH HOH . F 5 HOH A 46 946 90 HOH HOH . F 5 HOH A 47 947 69 HOH HOH . F 5 HOH A 48 948 30 HOH HOH . F 5 HOH A 49 949 85 HOH HOH . F 5 HOH A 50 950 89 HOH HOH . F 5 HOH A 51 951 56 HOH HOH . F 5 HOH A 52 952 115 HOH HOH . F 5 HOH A 53 953 58 HOH HOH . F 5 HOH A 54 954 52 HOH HOH . F 5 HOH A 55 955 11 HOH HOH . F 5 HOH A 56 956 81 HOH HOH . F 5 HOH A 57 957 6 HOH HOH . F 5 HOH A 58 958 155 HOH HOH . F 5 HOH A 59 959 87 HOH HOH . F 5 HOH A 60 960 25 HOH HOH . F 5 HOH A 61 961 18 HOH HOH . F 5 HOH A 62 962 50 HOH HOH . F 5 HOH A 63 963 48 HOH HOH . F 5 HOH A 64 964 26 HOH HOH . F 5 HOH A 65 965 76 HOH HOH . F 5 HOH A 66 966 95 HOH HOH . F 5 HOH A 67 967 106 HOH HOH . F 5 HOH A 68 968 70 HOH HOH . F 5 HOH A 69 969 79 HOH HOH . F 5 HOH A 70 970 45 HOH HOH . F 5 HOH A 71 971 27 HOH HOH . F 5 HOH A 72 972 120 HOH HOH . F 5 HOH A 73 973 36 HOH HOH . F 5 HOH A 74 974 49 HOH HOH . F 5 HOH A 75 975 112 HOH HOH . F 5 HOH A 76 976 93 HOH HOH . F 5 HOH A 77 977 80 HOH HOH . F 5 HOH A 78 978 71 HOH HOH . F 5 HOH A 79 979 28 HOH HOH . F 5 HOH A 80 980 1 HOH HOH . F 5 HOH A 81 981 137 HOH HOH . F 5 HOH A 82 982 60 HOH HOH . F 5 HOH A 83 983 119 HOH HOH . F 5 HOH A 84 984 107 HOH HOH . F 5 HOH A 85 985 146 HOH HOH . F 5 HOH A 86 986 15 HOH HOH . F 5 HOH A 87 987 131 HOH HOH . F 5 HOH A 88 988 37 HOH HOH . F 5 HOH A 89 989 145 HOH HOH . F 5 HOH A 90 990 46 HOH HOH . F 5 HOH A 91 991 73 HOH HOH . F 5 HOH A 92 992 92 HOH HOH . F 5 HOH A 93 993 151 HOH HOH . F 5 HOH A 94 994 121 HOH HOH . F 5 HOH A 95 995 101 HOH HOH . F 5 HOH A 96 996 86 HOH HOH . F 5 HOH A 97 997 74 HOH HOH . F 5 HOH A 98 998 88 HOH HOH . F 5 HOH A 99 999 35 HOH HOH . F 5 HOH A 100 1000 105 HOH HOH . F 5 HOH A 101 1001 96 HOH HOH . F 5 HOH A 102 1002 84 HOH HOH . F 5 HOH A 103 1003 128 HOH HOH . F 5 HOH A 104 1004 130 HOH HOH . F 5 HOH A 105 1005 108 HOH HOH . F 5 HOH A 106 1006 111 HOH HOH . F 5 HOH A 107 1007 154 HOH HOH . F 5 HOH A 108 1008 113 HOH HOH . F 5 HOH A 109 1009 125 HOH HOH . F 5 HOH A 110 1010 143 HOH HOH . F 5 HOH A 111 1011 141 HOH HOH . F 5 HOH A 112 1012 104 HOH HOH . F 5 HOH A 113 1013 147 HOH HOH . F 5 HOH A 114 1014 72 HOH HOH . F 5 HOH A 115 1015 138 HOH HOH . F 5 HOH A 116 1016 149 HOH HOH . F 5 HOH A 117 1017 133 HOH HOH . F 5 HOH A 118 1018 157 HOH HOH . G 5 HOH B 1 601 63 HOH HOH . G 5 HOH B 2 602 44 HOH HOH . G 5 HOH B 3 603 10 HOH HOH . G 5 HOH B 4 604 110 HOH HOH . G 5 HOH B 5 605 144 HOH HOH . G 5 HOH B 6 606 32 HOH HOH . G 5 HOH B 7 607 124 HOH HOH . G 5 HOH B 8 608 109 HOH HOH . G 5 HOH B 9 609 100 HOH HOH . G 5 HOH B 10 610 123 HOH HOH . G 5 HOH B 11 611 14 HOH HOH . G 5 HOH B 12 612 98 HOH HOH . G 5 HOH B 13 613 3 HOH HOH . G 5 HOH B 14 614 13 HOH HOH . G 5 HOH B 15 615 19 HOH HOH . G 5 HOH B 16 616 67 HOH HOH . G 5 HOH B 17 617 153 HOH HOH . G 5 HOH B 18 618 17 HOH HOH . G 5 HOH B 19 619 116 HOH HOH . G 5 HOH B 20 620 22 HOH HOH . G 5 HOH B 21 621 82 HOH HOH . G 5 HOH B 22 622 134 HOH HOH . G 5 HOH B 23 623 43 HOH HOH . G 5 HOH B 24 624 148 HOH HOH . G 5 HOH B 25 625 57 HOH HOH . G 5 HOH B 26 626 122 HOH HOH . G 5 HOH B 27 627 102 HOH HOH . G 5 HOH B 28 628 68 HOH HOH . G 5 HOH B 29 629 64 HOH HOH . G 5 HOH B 30 630 54 HOH HOH . G 5 HOH B 31 631 142 HOH HOH . G 5 HOH B 32 632 152 HOH HOH . G 5 HOH B 33 633 129 HOH HOH . G 5 HOH B 34 634 139 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 NAG . . . D 4 10.566 20.243 82.044 1 78.16 ? C1 NAG 804 A 1 HETATM 2 C C2 NAG . . . D 4 11.849 20.862 82.6 1 89.27 ? C2 NAG 804 A 1 HETATM 3 C C3 NAG . . . D 4 12.791 21.237 81.462 1 96.72 ? C3 NAG 804 A 1 HETATM 4 C C4 NAG . . . D 4 13.13 19.994 80.65 1 97.13 ? C4 NAG 804 A 1 HETATM 5 C C5 NAG . . . D 4 11.843 19.355 80.112 1 92.05 ? C5 NAG 804 A 1 HETATM 6 C C6 NAG . . . D 4 12.089 18.025 79.431 1 84.47 ? C6 NAG 804 A 1 HETATM 7 C C7 NAG . . . D 4 11.638 21.931 84.778 1 77.57 ? C7 NAG 804 A 1 HETATM 8 C C8 NAG . . . D 4 11.329 23.191 85.53 1 74.78 ? C8 NAG 804 A 1 HETATM 9 N N2 NAG . . . D 4 11.572 22.009 83.447 1 85.69 ? N2 NAG 804 A 1 HETATM 10 O O3 NAG . . . D 4 13.981 21.812 81.993 1 97.35 ? O3 NAG 804 A 1 HETATM 11 O O4 NAG . . . D 4 14.035 20.311 79.594 1 96.97 ? O4 NAG 804 A 1 HETATM 12 O O5 NAG . . . D 4 10.905 19.099 81.177 1 87.42 ? O5 NAG 804 A 1 HETATM 13 O O6 NAG . . . D 4 12.372 17.002 80.376 1 76.55 ? O6 NAG 804 A 1 HETATM 14 O O7 NAG . . . D 4 11.933 20.885 85.35 1 71.9 ? O7 NAG 804 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 14 #