data_1Y52 # _model_server_result.job_id 6Hi-a4KCUbLvFN2Oz0nTog _model_server_result.datetime_utc '2025-03-01 07:36:05' _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 1y52 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":905}' # _entry.id 1Y52 # _exptl.entry_id 1Y52 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 90 _cell.entry_id 1Y52 _cell.length_a 80.963 _cell.length_b 80.963 _cell.length_c 140.698 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y52 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 80.963 80.963 70.349 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 F N N ? 2 G N 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 4 X CYS 4 1_555 A SG CYS 81 X CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf2 B SG CYS 4 Y CYS 204 1_555 B SG CYS 81 Y CYS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? covale ? covale1 A ND2 ASN 43 X ASN 43 1_555 C C1 NAG . X NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 117 X ASN 117 1_555 D C1 NAG . X NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale3 B ND2 ASN 43 Y ASN 243 1_555 F C1 NAG . Y NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B ND2 ASN 117 Y ASN 317 1_555 G C1 NAG . Y NAG 906 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 270 n n C1 O1 NAG sing 271 n n C1 O5 NAG sing 272 n n C1 H1 NAG sing 273 n n C2 C3 NAG sing 274 n n C2 N2 NAG sing 275 n n C2 H2 NAG sing 276 n n C3 C4 NAG sing 277 n n C3 O3 NAG sing 278 n n C3 H3 NAG sing 279 n n C4 C5 NAG sing 280 n n C4 O4 NAG sing 281 n n C4 H4 NAG sing 282 n n C5 C6 NAG sing 283 n n C5 O5 NAG sing 284 n n C5 H5 NAG sing 285 n n C6 O6 NAG sing 286 n n C6 H61 NAG sing 287 n n C6 H62 NAG sing 288 n n C7 C8 NAG sing 289 n n C7 N2 NAG sing 290 n n C7 O7 NAG doub 291 n n C8 H81 NAG sing 292 n n C8 H82 NAG sing 293 n n C8 H83 NAG sing 294 n n N2 HN2 NAG sing 295 n n O1 HO1 NAG sing 296 n n O3 HO3 NAG sing 297 n n O4 HO4 NAG sing 298 n n O6 HO6 NAG sing 299 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 1Y52 _atom_sites.fract_transf_matrix[1][1] 0.012351 _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] 0.012351 _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] 0.007107 _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 2 NAG X 1 901 901 NAG NAG . D 2 NAG X 1 905 905 NAG NAG . E 3 BTN X 1 801 801 BTN BTN . F 2 NAG Y 1 902 902 NAG NAG . G 2 NAG Y 1 906 906 NAG NAG . H 3 BTN Y 1 802 802 BTN BTN . I 4 HOH X 1 906 1 HOH HOH . I 4 HOH X 2 907 5 HOH HOH . I 4 HOH X 3 908 7 HOH HOH . I 4 HOH X 4 909 9 HOH HOH . I 4 HOH X 5 910 11 HOH HOH . I 4 HOH X 6 911 15 HOH HOH . I 4 HOH X 7 912 16 HOH HOH . I 4 HOH X 8 913 17 HOH HOH . I 4 HOH X 9 914 18 HOH HOH . I 4 HOH X 10 915 19 HOH HOH . I 4 HOH X 11 916 21 HOH HOH . I 4 HOH X 12 917 22 HOH HOH . I 4 HOH X 13 918 23 HOH HOH . I 4 HOH X 14 919 25 HOH HOH . I 4 HOH X 15 920 26 HOH HOH . I 4 HOH X 16 921 30 HOH HOH . I 4 HOH X 17 922 31 HOH HOH . I 4 HOH X 18 923 32 HOH HOH . I 4 HOH X 19 924 34 HOH HOH . I 4 HOH X 20 925 36 HOH HOH . I 4 HOH X 21 926 42 HOH HOH . I 4 HOH X 22 927 45 HOH HOH . I 4 HOH X 23 928 48 HOH HOH . I 4 HOH X 24 929 50 HOH HOH . I 4 HOH X 25 930 51 HOH HOH . I 4 HOH X 26 931 56 HOH HOH . I 4 HOH X 27 932 57 HOH HOH . I 4 HOH X 28 933 58 HOH HOH . I 4 HOH X 29 934 60 HOH HOH . I 4 HOH X 30 935 63 HOH HOH . I 4 HOH X 31 936 65 HOH HOH . I 4 HOH X 32 937 66 HOH HOH . I 4 HOH X 33 938 68 HOH HOH . I 4 HOH X 34 939 71 HOH HOH . I 4 HOH X 35 940 72 HOH HOH . I 4 HOH X 36 941 74 HOH HOH . I 4 HOH X 37 942 75 HOH HOH . I 4 HOH X 38 943 76 HOH HOH . I 4 HOH X 39 944 80 HOH HOH . I 4 HOH X 40 945 81 HOH HOH . I 4 HOH X 41 946 82 HOH HOH . I 4 HOH X 42 947 84 HOH HOH . I 4 HOH X 43 948 88 HOH HOH . I 4 HOH X 44 949 91 HOH HOH . I 4 HOH X 45 950 92 HOH HOH . I 4 HOH X 46 951 93 HOH HOH . I 4 HOH X 47 952 95 HOH HOH . I 4 HOH X 48 953 96 HOH HOH . I 4 HOH X 49 954 97 HOH HOH . I 4 HOH X 50 955 98 HOH HOH . I 4 HOH X 51 956 99 HOH HOH . I 4 HOH X 52 957 100 HOH HOH . I 4 HOH X 53 958 101 HOH HOH . I 4 HOH X 54 959 102 HOH HOH . I 4 HOH X 55 960 106 HOH HOH . I 4 HOH X 56 961 107 HOH HOH . I 4 HOH X 57 962 108 HOH HOH . I 4 HOH X 58 963 109 HOH HOH . I 4 HOH X 59 964 112 HOH HOH . I 4 HOH X 60 965 113 HOH HOH . I 4 HOH X 61 966 114 HOH HOH . I 4 HOH X 62 967 116 HOH HOH . I 4 HOH X 63 968 118 HOH HOH . I 4 HOH X 64 969 120 HOH HOH . I 4 HOH X 65 970 121 HOH HOH . J 4 HOH Y 1 2 2 HOH HOH . J 4 HOH Y 2 3 3 HOH HOH . J 4 HOH Y 3 4 4 HOH HOH . J 4 HOH Y 4 6 6 HOH HOH . J 4 HOH Y 5 8 8 HOH HOH . J 4 HOH Y 6 10 10 HOH HOH . J 4 HOH Y 7 12 12 HOH HOH . J 4 HOH Y 8 13 13 HOH HOH . J 4 HOH Y 9 14 14 HOH HOH . J 4 HOH Y 10 20 20 HOH HOH . J 4 HOH Y 11 24 24 HOH HOH . J 4 HOH Y 12 27 27 HOH HOH . J 4 HOH Y 13 28 28 HOH HOH . J 4 HOH Y 14 29 29 HOH HOH . J 4 HOH Y 15 33 33 HOH HOH . J 4 HOH Y 16 35 35 HOH HOH . J 4 HOH Y 17 37 37 HOH HOH . J 4 HOH Y 18 38 38 HOH HOH . J 4 HOH Y 19 39 39 HOH HOH . J 4 HOH Y 20 40 40 HOH HOH . J 4 HOH Y 21 41 41 HOH HOH . J 4 HOH Y 22 43 43 HOH HOH . J 4 HOH Y 23 44 44 HOH HOH . J 4 HOH Y 24 46 46 HOH HOH . J 4 HOH Y 25 47 47 HOH HOH . J 4 HOH Y 26 49 49 HOH HOH . J 4 HOH Y 27 52 52 HOH HOH . J 4 HOH Y 28 53 53 HOH HOH . J 4 HOH Y 29 54 54 HOH HOH . J 4 HOH Y 30 55 55 HOH HOH . J 4 HOH Y 31 59 59 HOH HOH . J 4 HOH Y 32 61 61 HOH HOH . J 4 HOH Y 33 62 62 HOH HOH . J 4 HOH Y 34 64 64 HOH HOH . J 4 HOH Y 35 67 67 HOH HOH . J 4 HOH Y 36 69 69 HOH HOH . J 4 HOH Y 37 70 70 HOH HOH . J 4 HOH Y 38 73 73 HOH HOH . J 4 HOH Y 39 77 77 HOH HOH . J 4 HOH Y 40 78 78 HOH HOH . J 4 HOH Y 41 79 79 HOH HOH . J 4 HOH Y 42 83 83 HOH HOH . J 4 HOH Y 43 85 85 HOH HOH . J 4 HOH Y 44 86 86 HOH HOH . J 4 HOH Y 45 87 87 HOH HOH . J 4 HOH Y 46 89 89 HOH HOH . J 4 HOH Y 47 90 90 HOH HOH . J 4 HOH Y 48 94 94 HOH HOH . J 4 HOH Y 49 103 103 HOH HOH . J 4 HOH Y 50 104 104 HOH HOH . J 4 HOH Y 51 105 105 HOH HOH . J 4 HOH Y 52 110 110 HOH HOH . J 4 HOH Y 53 111 111 HOH HOH . J 4 HOH Y 54 115 115 HOH HOH . J 4 HOH Y 55 117 117 HOH HOH . J 4 HOH Y 56 119 119 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 2 76.405 2.716 30.748 0.5 39.08 ? C1 NAG 905 X 1 HETATM 2 C C2 NAG . . . D 2 76.879 1.419 30.089 0.5 40.68 ? C2 NAG 905 X 1 HETATM 3 C C3 NAG . . . D 2 77.683 0.542 31.056 0.5 41.58 ? C3 NAG 905 X 1 HETATM 4 C C4 NAG . . . D 2 78.746 1.363 31.785 0.5 41.86 ? C4 NAG 905 X 1 HETATM 5 C C5 NAG . . . D 2 78.116 2.62 32.387 0.5 41.93 ? C5 NAG 905 X 1 HETATM 6 C C6 NAG . . . D 2 79.129 3.515 33.088 0.5 41.82 ? C6 NAG 905 X 1 HETATM 7 C C7 NAG . . . D 2 75.508 0.647 28.252 0.5 41 ? C7 NAG 905 X 1 HETATM 8 C C8 NAG . . . D 2 74.436 -0.255 27.74 0.5 40.17 ? C8 NAG 905 X 1 HETATM 9 N N2 NAG . . . D 2 75.733 0.684 29.562 0.5 41.5 ? N2 NAG 905 X 1 HETATM 10 O O3 NAG . . . D 2 78.3 -0.498 30.332 0.5 41.84 ? O3 NAG 905 X 1 HETATM 11 O O4 NAG . . . D 2 79.335 0.587 32.806 0.5 42.38 ? O4 NAG 905 X 1 HETATM 12 O O5 NAG . . . D 2 77.514 3.358 31.346 0.5 39.76 ? O5 NAG 905 X 1 HETATM 13 O O6 NAG . . . D 2 80.068 3.979 32.142 0.5 42.83 ? O6 NAG 905 X 1 HETATM 14 O O7 NAG . . . D 2 76.153 1.324 27.466 0.5 43.28 ? O7 NAG 905 X 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #