data_2CKM # _model_server_result.job_id x-DgX1qSb7D9WKWXNIdt9Q _model_server_result.datetime_utc '2024-12-03 04:25:35' _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 2ckm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1537}' # _entry.id 2CKM # _exptl.entry_id 2CKM _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 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 2CKM _cell.length_a 111.884 _cell.length_b 111.884 _cell.length_c 137.413 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2CKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 137.413 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D 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 67 A CYS 67 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf2 A SG CYS 254 A CYS 254 1_555 A SG CYS 265 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 402 A CYS 402 1_555 A SG CYS 521 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 59 A ASN 59 1_555 C C1 NAG . A NAG 1537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale2 A ND2 ASN 416 A ASN 416 1_555 D C1 NAG . A NAG 1538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? # _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 319 n n C1 O1 NAG sing 320 n n C1 O5 NAG sing 321 n n C1 H1 NAG sing 322 n n C2 C3 NAG sing 323 n n C2 N2 NAG sing 324 n n C2 H2 NAG sing 325 n n C3 C4 NAG sing 326 n n C3 O3 NAG sing 327 n n C3 H3 NAG sing 328 n n C4 C5 NAG sing 329 n n C4 O4 NAG sing 330 n n C4 H4 NAG sing 331 n n C5 C6 NAG sing 332 n n C5 O5 NAG sing 333 n n C5 H5 NAG sing 334 n n C6 O6 NAG sing 335 n n C6 H61 NAG sing 336 n n C6 H62 NAG sing 337 n n C7 C8 NAG sing 338 n n C7 N2 NAG sing 339 n n C7 O7 NAG doub 340 n n C8 H81 NAG sing 341 n n C8 H82 NAG sing 342 n n C8 H83 NAG sing 343 n n N2 HN2 NAG sing 344 n n O1 HO1 NAG sing 345 n n O3 HO3 NAG sing 346 n n O4 HO4 NAG sing 347 n n O6 HO6 NAG sing 348 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 2CKM _atom_sites.fract_transf_matrix[1][1] 0.008938 _atom_sites.fract_transf_matrix[1][2] 0.00516 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010321 _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] 0.007277 _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 AA7 A 1 1536 1536 AA7 AA7 . C 3 NAG A 1 1537 1537 NAG NAG . D 3 NAG A 1 1538 1538 NAG NAG . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 HOH HOH . E 4 HOH A 45 2045 2045 HOH HOH . E 4 HOH A 46 2046 2046 HOH HOH . E 4 HOH A 47 2047 2047 HOH HOH . E 4 HOH A 48 2048 2048 HOH HOH . E 4 HOH A 49 2049 2049 HOH HOH . E 4 HOH A 50 2050 2050 HOH HOH . E 4 HOH A 51 2051 2051 HOH HOH . E 4 HOH A 52 2052 2052 HOH HOH . E 4 HOH A 53 2053 2053 HOH HOH . E 4 HOH A 54 2054 2054 HOH HOH . E 4 HOH A 55 2055 2055 HOH HOH . E 4 HOH A 56 2056 2056 HOH HOH . E 4 HOH A 57 2057 2057 HOH HOH . E 4 HOH A 58 2058 2058 HOH HOH . E 4 HOH A 59 2059 2059 HOH HOH . E 4 HOH A 60 2060 2060 HOH HOH . E 4 HOH A 61 2061 2061 HOH HOH . E 4 HOH A 62 2062 2062 HOH HOH . E 4 HOH A 63 2063 2063 HOH HOH . E 4 HOH A 64 2064 2064 HOH HOH . E 4 HOH A 65 2065 2065 HOH HOH . E 4 HOH A 66 2066 2066 HOH HOH . E 4 HOH A 67 2067 2067 HOH HOH . E 4 HOH A 68 2068 2068 HOH HOH . E 4 HOH A 69 2069 2069 HOH HOH . E 4 HOH A 70 2070 2070 HOH HOH . E 4 HOH A 71 2071 2071 HOH HOH . E 4 HOH A 72 2072 2072 HOH HOH . E 4 HOH A 73 2073 2073 HOH HOH . E 4 HOH A 74 2074 2074 HOH HOH . E 4 HOH A 75 2075 2075 HOH HOH . E 4 HOH A 76 2076 2076 HOH HOH . E 4 HOH A 77 2077 2077 HOH HOH . E 4 HOH A 78 2078 2078 HOH HOH . E 4 HOH A 79 2079 2079 HOH HOH . E 4 HOH A 80 2080 2080 HOH HOH . E 4 HOH A 81 2081 2081 HOH HOH . E 4 HOH A 82 2082 2082 HOH HOH . E 4 HOH A 83 2083 2083 HOH HOH . E 4 HOH A 84 2084 2084 HOH HOH . E 4 HOH A 85 2085 2085 HOH HOH . E 4 HOH A 86 2086 2086 HOH HOH . E 4 HOH A 87 2087 2087 HOH HOH . E 4 HOH A 88 2088 2088 HOH HOH . E 4 HOH A 89 2089 2089 HOH HOH . E 4 HOH A 90 2090 2090 HOH HOH . E 4 HOH A 91 2091 2091 HOH HOH . E 4 HOH A 92 2092 2092 HOH HOH . E 4 HOH A 93 2093 2093 HOH HOH . E 4 HOH A 94 2094 2094 HOH HOH . E 4 HOH A 95 2095 2095 HOH HOH . E 4 HOH A 96 2096 2096 HOH HOH . E 4 HOH A 97 2097 2097 HOH HOH . E 4 HOH A 98 2098 2098 HOH HOH . E 4 HOH A 99 2099 2099 HOH HOH . E 4 HOH A 100 2100 2100 HOH HOH . E 4 HOH A 101 2101 2101 HOH HOH . E 4 HOH A 102 2102 2102 HOH HOH . E 4 HOH A 103 2103 2103 HOH HOH . E 4 HOH A 104 2104 2104 HOH HOH . E 4 HOH A 105 2105 2105 HOH HOH . E 4 HOH A 106 2106 2106 HOH HOH . E 4 HOH A 107 2107 2107 HOH HOH . E 4 HOH A 108 2108 2108 HOH HOH . E 4 HOH A 109 2109 2109 HOH HOH . E 4 HOH A 110 2110 2110 HOH HOH . E 4 HOH A 111 2111 2111 HOH HOH . E 4 HOH A 112 2112 2112 HOH HOH . E 4 HOH A 113 2113 2113 HOH HOH . E 4 HOH A 114 2114 2114 HOH HOH . E 4 HOH A 115 2115 2115 HOH HOH . E 4 HOH A 116 2116 2116 HOH HOH . E 4 HOH A 117 2117 2117 HOH HOH . E 4 HOH A 118 2118 2118 HOH HOH . E 4 HOH A 119 2119 2119 HOH HOH . E 4 HOH A 120 2120 2120 HOH HOH . E 4 HOH A 121 2121 2121 HOH HOH . E 4 HOH A 122 2122 2122 HOH HOH . E 4 HOH A 123 2123 2123 HOH HOH . E 4 HOH A 124 2124 2124 HOH HOH . E 4 HOH A 125 2125 2125 HOH HOH . E 4 HOH A 126 2126 2126 HOH HOH . E 4 HOH A 127 2127 2127 HOH HOH . E 4 HOH A 128 2128 2128 HOH HOH . E 4 HOH A 129 2129 2129 HOH HOH . E 4 HOH A 130 2130 2130 HOH HOH . E 4 HOH A 131 2131 2131 HOH HOH . E 4 HOH A 132 2132 2132 HOH HOH . E 4 HOH A 133 2133 2133 HOH HOH . E 4 HOH A 134 2134 2134 HOH HOH . E 4 HOH A 135 2135 2135 HOH HOH . E 4 HOH A 136 2136 2136 HOH HOH . E 4 HOH A 137 2137 2137 HOH HOH . E 4 HOH A 138 2138 2138 HOH HOH . E 4 HOH A 139 2139 2139 HOH HOH . E 4 HOH A 140 2140 2140 HOH HOH . E 4 HOH A 141 2141 2141 HOH HOH . E 4 HOH A 142 2142 2142 HOH HOH . E 4 HOH A 143 2143 2143 HOH HOH . E 4 HOH A 144 2144 2144 HOH HOH . E 4 HOH A 145 2145 2145 HOH HOH . E 4 HOH A 146 2146 2146 HOH HOH . E 4 HOH A 147 2147 2147 HOH HOH . E 4 HOH A 148 2148 2148 HOH HOH . E 4 HOH A 149 2149 2149 HOH HOH . E 4 HOH A 150 2150 2150 HOH HOH . E 4 HOH A 151 2151 2151 HOH HOH . E 4 HOH A 152 2152 2152 HOH HOH . E 4 HOH A 153 2153 2153 HOH HOH . E 4 HOH A 154 2154 2154 HOH HOH . E 4 HOH A 155 2155 2155 HOH HOH . E 4 HOH A 156 2156 2156 HOH HOH . E 4 HOH A 157 2157 2157 HOH HOH . E 4 HOH A 158 2158 2158 HOH HOH . E 4 HOH A 159 2159 2159 HOH HOH . E 4 HOH A 160 2160 2160 HOH HOH . E 4 HOH A 161 2161 2161 HOH HOH . E 4 HOH A 162 2162 2162 HOH HOH . E 4 HOH A 163 2163 2163 HOH HOH . E 4 HOH A 164 2164 2164 HOH HOH . E 4 HOH A 165 2165 2165 HOH HOH . E 4 HOH A 166 2166 2166 HOH HOH . E 4 HOH A 167 2167 2167 HOH HOH . E 4 HOH A 168 2168 2168 HOH HOH . E 4 HOH A 169 2169 2169 HOH HOH . E 4 HOH A 170 2170 2170 HOH HOH . E 4 HOH A 171 2171 2171 HOH HOH . E 4 HOH A 172 2172 2172 HOH HOH . E 4 HOH A 173 2173 2173 HOH HOH . E 4 HOH A 174 2174 2174 HOH HOH . E 4 HOH A 175 2175 2175 HOH HOH . E 4 HOH A 176 2176 2176 HOH HOH . E 4 HOH A 177 2177 2177 HOH HOH . E 4 HOH A 178 2178 2178 HOH HOH . E 4 HOH A 179 2179 2179 HOH HOH . E 4 HOH A 180 2180 2180 HOH HOH . E 4 HOH A 181 2181 2181 HOH HOH . E 4 HOH A 182 2182 2182 HOH HOH . E 4 HOH A 183 2183 2183 HOH HOH . E 4 HOH A 184 2184 2184 HOH HOH . E 4 HOH A 185 2185 2185 HOH HOH . E 4 HOH A 186 2186 2186 HOH HOH . E 4 HOH A 187 2187 2187 HOH HOH . E 4 HOH A 188 2188 2188 HOH HOH . E 4 HOH A 189 2189 2189 HOH HOH . E 4 HOH A 190 2190 2190 HOH HOH . E 4 HOH A 191 2191 2191 HOH HOH . E 4 HOH A 192 2192 2192 HOH HOH . E 4 HOH A 193 2193 2193 HOH HOH . E 4 HOH A 194 2194 2194 HOH HOH . E 4 HOH A 195 2195 2195 HOH HOH . E 4 HOH A 196 2196 2196 HOH HOH . E 4 HOH A 197 2197 2197 HOH HOH . E 4 HOH A 198 2198 2198 HOH HOH . E 4 HOH A 199 2199 2199 HOH HOH . E 4 HOH A 200 2200 2200 HOH HOH . E 4 HOH A 201 2201 2201 HOH HOH . E 4 HOH A 202 2202 2202 HOH HOH . E 4 HOH A 203 2203 2203 HOH HOH . E 4 HOH A 204 2204 2204 HOH HOH . E 4 HOH A 205 2205 2205 HOH HOH . E 4 HOH A 206 2207 2207 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 -18.72 83.489 50.159 1 72.72 ? C1 NAG 1537 A 1 HETATM 2 C C2 NAG . . . C 3 -19.667 84.69 50.03 1 75.58 ? C2 NAG 1537 A 1 HETATM 3 C C3 NAG . . . C 3 -19.219 85.801 51.007 1 77.59 ? C3 NAG 1537 A 1 HETATM 4 C C4 NAG . . . C 3 -19.308 85.238 52.443 1 78.8 ? C4 NAG 1537 A 1 HETATM 5 C C5 NAG . . . C 3 -18.376 84.006 52.525 1 77.39 ? C5 NAG 1537 A 1 HETATM 6 C C6 NAG . . . C 3 -18.252 83.337 53.915 1 77.19 ? C6 NAG 1537 A 1 HETATM 7 C C7 NAG . . . C 3 -20.735 84.722 47.873 1 75.62 ? C7 NAG 1537 A 1 HETATM 8 C C8 NAG . . . C 3 -21.031 85.53 46.62 1 74.91 ? C8 NAG 1537 A 1 HETATM 9 N N2 NAG . . . C 3 -19.748 85.159 48.66 1 75.46 ? N2 NAG 1537 A 1 HETATM 10 O O3 NAG . . . C 3 -20.052 86.948 50.876 1 78.87 ? O3 NAG 1537 A 1 HETATM 11 O O4 NAG . . . C 3 -18.959 86.235 53.419 1 81.05 ? O4 NAG 1537 A 1 HETATM 12 O O5 NAG . . . C 3 -18.783 82.998 51.534 1 75.7 ? O5 NAG 1537 A 1 HETATM 13 O O6 NAG . . . C 3 -19.396 82.571 54.283 1 77.42 ? O6 NAG 1537 A 1 HETATM 14 O O7 NAG . . . C 3 -21.402 83.711 48.12 1 74.76 ? O7 NAG 1537 A 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #