data_2YGN # _model_server_result.job_id u05NMdXiHc_gAQl8htAx2Q _model_server_result.datetime_utc '2025-07-28 11:03:52' _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 2ygn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1180}' # _entry.id 2YGN # _exptl.entry_id 2YGN _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 90 _cell.entry_id 2YGN _cell.length_a 49.912 _cell.length_b 134.138 _cell.length_c 60.378 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGN _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 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 _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' 6_445 -x-1/2,-y-1/2,z -1 0 0 0 -1 0 0 0 1 -24.956 -67.069 0 # _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 109 A CYS 140 1_555 A SG CYS 146 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A C GLY 30 A GLY 61 1_555 A N MLY 31 A MLY 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale2 A C MLY 31 A MLY 62 1_555 A N MET 32 A MET 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale3 A C ARG 40 A ARG 71 1_555 A N MLY 41 A MLY 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale4 A C MLY 41 A MLY 72 1_555 A N ALA 42 A ALA 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale5 A ND2 ASN 57 A ASN 88 1_555 C C1 NAG . A NAG 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 A C ASP 79 A ASP 110 1_555 A N MLY 80 A MLY 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 A C MLY 80 A MLY 111 1_555 A N GLY 81 A GLY 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale8 A C HIS 98 A HIS 129 1_555 A N MLY 99 A MLY 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale9 A C MLY 99 A MLY 130 1_555 A N ALA 100 A ALA 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale10 A C GLY 111 A GLY 142 1_555 A N MLY 112 A MLY 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale11 A C MLY 112 A MLY 143 1_555 A N GLN 113 A GLN 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale12 A C LEU 134 A LEU 165 1_555 A N MLY 135 A MLY 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale13 A C MLY 135 A MLY 166 1_555 A N THR 136 A THR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 272 n n C1 O1 NAG sing 273 n n C1 O5 NAG sing 274 n n C1 H1 NAG sing 275 n n C2 C3 NAG sing 276 n n C2 N2 NAG sing 277 n n C2 H2 NAG sing 278 n n C3 C4 NAG sing 279 n n C3 O3 NAG sing 280 n n C3 H3 NAG sing 281 n n C4 C5 NAG sing 282 n n C4 O4 NAG sing 283 n n C4 H4 NAG sing 284 n n C5 C6 NAG sing 285 n n C5 O5 NAG sing 286 n n C5 H5 NAG sing 287 n n C6 O6 NAG sing 288 n n C6 H61 NAG sing 289 n n C6 H62 NAG sing 290 n n C7 C8 NAG sing 291 n n C7 N2 NAG sing 292 n n C7 O7 NAG doub 293 n n C8 H81 NAG sing 294 n n C8 H82 NAG sing 295 n n C8 H83 NAG sing 296 n n N2 HN2 NAG sing 297 n n O1 HO1 NAG sing 298 n n O3 HO3 NAG sing 299 n n O4 HO4 NAG sing 300 n n O6 HO6 NAG sing 301 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 2YGN _atom_sites.fract_transf_matrix[1][1] 0.020035 _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] 0.007455 _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] 0.016562 _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 B 2 PCF A 1 1179 1179 PCF PCF . C 3 NAG A 1 1180 1180 NAG NAG . D 4 ACT A 1 1181 1181 ACT ACT . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 HOH HOH . E 5 HOH A 80 2080 2080 HOH HOH . E 5 HOH A 81 2081 2081 HOH HOH . E 5 HOH A 82 2082 2082 HOH HOH . E 5 HOH A 83 2083 2083 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 . . . C 3 -6.288 -10.261 4.294 1 56.64 ? C1 NAG 1180 A 1 HETATM 2 C C2 NAG . . . C 3 -5.646 -9.034 3.582 1 59.56 ? C2 NAG 1180 A 1 HETATM 3 C C3 NAG . . . C 3 -6.767 -8.348 2.717 1 62.12 ? C3 NAG 1180 A 1 HETATM 4 C C4 NAG . . . C 3 -7.496 -9.381 1.795 1 62.41 ? C4 NAG 1180 A 1 HETATM 5 C C5 NAG . . . C 3 -7.962 -10.597 2.628 1 60.43 ? C5 NAG 1180 A 1 HETATM 6 C C6 NAG . . . C 3 -8.606 -11.699 1.745 1 61.46 ? C6 NAG 1180 A 1 HETATM 7 C C7 NAG . . . C 3 -3.617 -7.885 4.602 1 62.4 ? C7 NAG 1180 A 1 HETATM 8 C C8 NAG . . . C 3 -3.211 -6.929 5.683 1 63.72 ? C8 NAG 1180 A 1 HETATM 9 N N2 NAG . . . C 3 -4.956 -8.141 4.541 1 60.69 ? N2 NAG 1180 A 1 HETATM 10 O O3 NAG . . . C 3 -6.153 -7.337 1.9 1 65.43 ? O3 NAG 1180 A 1 HETATM 11 O O4 NAG . . . C 3 -8.67 -8.785 1.216 1 65.91 ? O4 NAG 1180 A 1 HETATM 12 O O5 NAG . . . C 3 -6.83 -11.165 3.339 1 57.82 ? O5 NAG 1180 A 1 HETATM 13 O O6 NAG . . . C 3 -7.637 -12.364 0.897 1 63.9 ? O6 NAG 1180 A 1 HETATM 14 O O7 NAG . . . C 3 -2.792 -8.37 3.846 1 64.32 ? O7 NAG 1180 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #