data_1YJD # _model_server_result.job_id r0u9ViUelwN4F9B_u5KykA _model_server_result.datetime_utc '2024-12-27 14:54:38' _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 1yjd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":203}' # _entry.id 1YJD # _exptl.entry_id 1YJD _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.45 _cell.angle_gamma 90 _cell.entry_id 1YJD _cell.length_a 191.219 _cell.length_b 47.417 _cell.length_c 71.842 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YJD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 185.644844 0 71.625427 # 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 ? 4 F 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 23 L CYS 23 1_555 A SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 134 L CYS 134 1_555 A SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 147 H CYS 147 1_555 B SG CYS 202 H CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 C SG CYS 24 C CYS 22 1_555 C SG CYS 96 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 C SG CYS 50 C CYS 48 1_555 C SG CYS 70 C CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 C ND2 ASN 21 C ASN 19 1_555 D C1 NAG . C NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 C ND2 ASN 55 C ASN 53 1_555 E C1 NAG . C NAG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 C ND2 ASN 89 C ASN 87 1_555 F C1 NAG . C NAG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 1YJD _atom_sites.fract_transf_matrix[1][1] 0.00523 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000407 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021089 _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] 0.013962 _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 C 1 201 201 NAG NAG . E 4 NAG C 1 202 202 NAG NAG . F 4 NAG C 1 203 203 NAG NAG . G 5 HOH L 1 213 1 HOH HOH . G 5 HOH L 2 214 3 HOH HOH . G 5 HOH L 3 215 6 HOH HOH . G 5 HOH L 4 216 7 HOH HOH . G 5 HOH L 5 217 10 HOH HOH . G 5 HOH L 6 218 13 HOH HOH . G 5 HOH L 7 219 14 HOH HOH . G 5 HOH L 8 220 18 HOH HOH . G 5 HOH L 9 221 19 HOH HOH . G 5 HOH L 10 222 22 HOH HOH . G 5 HOH L 11 223 23 HOH HOH . G 5 HOH L 12 224 24 HOH HOH . G 5 HOH L 13 225 25 HOH HOH . G 5 HOH L 14 226 26 HOH HOH . G 5 HOH L 15 227 27 HOH HOH . G 5 HOH L 16 228 28 HOH HOH . G 5 HOH L 17 229 29 HOH HOH . G 5 HOH L 18 230 31 HOH HOH . G 5 HOH L 19 231 35 HOH HOH . G 5 HOH L 20 232 36 HOH HOH . G 5 HOH L 21 233 37 HOH HOH . G 5 HOH L 22 234 38 HOH HOH . G 5 HOH L 23 235 40 HOH HOH . G 5 HOH L 24 236 42 HOH HOH . G 5 HOH L 25 237 44 HOH HOH . G 5 HOH L 26 238 45 HOH HOH . G 5 HOH L 27 239 49 HOH HOH . G 5 HOH L 28 240 51 HOH HOH . G 5 HOH L 29 241 53 HOH HOH . G 5 HOH L 30 242 54 HOH HOH . G 5 HOH L 31 243 55 HOH HOH . G 5 HOH L 32 244 56 HOH HOH . G 5 HOH L 33 245 57 HOH HOH . G 5 HOH L 34 246 62 HOH HOH . G 5 HOH L 35 247 63 HOH HOH . G 5 HOH L 36 248 65 HOH HOH . G 5 HOH L 37 249 74 HOH HOH . G 5 HOH L 38 250 78 HOH HOH . G 5 HOH L 39 251 82 HOH HOH . G 5 HOH L 40 252 84 HOH HOH . G 5 HOH L 41 253 87 HOH HOH . G 5 HOH L 42 254 88 HOH HOH . G 5 HOH L 43 255 89 HOH HOH . G 5 HOH L 44 256 94 HOH HOH . G 5 HOH L 45 257 96 HOH HOH . G 5 HOH L 46 258 98 HOH HOH . G 5 HOH L 47 259 99 HOH HOH . G 5 HOH L 48 260 100 HOH HOH . G 5 HOH L 49 261 101 HOH HOH . G 5 HOH L 50 262 102 HOH HOH . G 5 HOH L 51 263 105 HOH HOH . G 5 HOH L 52 264 108 HOH HOH . G 5 HOH L 53 265 110 HOH HOH . G 5 HOH L 54 266 111 HOH HOH . G 5 HOH L 55 267 112 HOH HOH . G 5 HOH L 56 268 113 HOH HOH . G 5 HOH L 57 269 115 HOH HOH . G 5 HOH L 58 270 117 HOH HOH . G 5 HOH L 59 271 123 HOH HOH . G 5 HOH L 60 272 128 HOH HOH . G 5 HOH L 61 273 134 HOH HOH . G 5 HOH L 62 274 136 HOH HOH . G 5 HOH L 63 275 140 HOH HOH . G 5 HOH L 64 276 144 HOH HOH . G 5 HOH L 65 277 147 HOH HOH . G 5 HOH L 66 278 148 HOH HOH . G 5 HOH L 67 279 150 HOH HOH . G 5 HOH L 68 280 154 HOH HOH . G 5 HOH L 69 281 158 HOH HOH . G 5 HOH L 70 282 159 HOH HOH . G 5 HOH L 71 283 162 HOH HOH . G 5 HOH L 72 284 165 HOH HOH . G 5 HOH L 73 285 167 HOH HOH . G 5 HOH L 74 286 169 HOH HOH . G 5 HOH L 75 287 171 HOH HOH . G 5 HOH L 76 288 173 HOH HOH . G 5 HOH L 77 289 176 HOH HOH . G 5 HOH L 78 290 178 HOH HOH . G 5 HOH L 79 291 182 HOH HOH . G 5 HOH L 80 292 183 HOH HOH . G 5 HOH L 81 293 185 HOH HOH . G 5 HOH L 82 294 186 HOH HOH . G 5 HOH L 83 295 188 HOH HOH . G 5 HOH L 84 296 191 HOH HOH . G 5 HOH L 85 297 192 HOH HOH . G 5 HOH L 86 298 193 HOH HOH . G 5 HOH L 87 299 200 HOH HOH . G 5 HOH L 88 300 202 HOH HOH . H 5 HOH H 1 223 2 HOH HOH . H 5 HOH H 2 224 4 HOH HOH . H 5 HOH H 3 225 8 HOH HOH . H 5 HOH H 4 226 11 HOH HOH . H 5 HOH H 5 227 12 HOH HOH . H 5 HOH H 6 228 15 HOH HOH . H 5 HOH H 7 229 16 HOH HOH . H 5 HOH H 8 230 17 HOH HOH . H 5 HOH H 9 231 20 HOH HOH . H 5 HOH H 10 232 21 HOH HOH . H 5 HOH H 11 233 32 HOH HOH . H 5 HOH H 12 234 33 HOH HOH . H 5 HOH H 13 235 34 HOH HOH . H 5 HOH H 14 236 43 HOH HOH . H 5 HOH H 15 237 46 HOH HOH . H 5 HOH H 16 238 47 HOH HOH . H 5 HOH H 17 239 48 HOH HOH . H 5 HOH H 18 240 52 HOH HOH . H 5 HOH H 19 241 58 HOH HOH . H 5 HOH H 20 242 60 HOH HOH . H 5 HOH H 21 243 61 HOH HOH . H 5 HOH H 22 244 64 HOH HOH . H 5 HOH H 23 245 66 HOH HOH . H 5 HOH H 24 246 69 HOH HOH . H 5 HOH H 25 247 70 HOH HOH . H 5 HOH H 26 248 72 HOH HOH . H 5 HOH H 27 249 73 HOH HOH . H 5 HOH H 28 250 75 HOH HOH . H 5 HOH H 29 251 77 HOH HOH . H 5 HOH H 30 252 79 HOH HOH . H 5 HOH H 31 253 80 HOH HOH . H 5 HOH H 32 254 90 HOH HOH . H 5 HOH H 33 255 91 HOH HOH . H 5 HOH H 34 256 92 HOH HOH . H 5 HOH H 35 257 93 HOH HOH . H 5 HOH H 36 258 95 HOH HOH . H 5 HOH H 37 259 97 HOH HOH . H 5 HOH H 38 260 103 HOH HOH . H 5 HOH H 39 261 104 HOH HOH . H 5 HOH H 40 262 109 HOH HOH . H 5 HOH H 41 263 114 HOH HOH . H 5 HOH H 42 264 118 HOH HOH . H 5 HOH H 43 265 120 HOH HOH . H 5 HOH H 44 266 122 HOH HOH . H 5 HOH H 45 267 124 HOH HOH . H 5 HOH H 46 268 126 HOH HOH . H 5 HOH H 47 269 127 HOH HOH . H 5 HOH H 48 270 129 HOH HOH . H 5 HOH H 49 271 130 HOH HOH . H 5 HOH H 50 272 131 HOH HOH . H 5 HOH H 51 273 132 HOH HOH . H 5 HOH H 52 274 135 HOH HOH . H 5 HOH H 53 275 138 HOH HOH . H 5 HOH H 54 276 142 HOH HOH . H 5 HOH H 55 277 143 HOH HOH . H 5 HOH H 56 278 149 HOH HOH . H 5 HOH H 57 279 153 HOH HOH . H 5 HOH H 58 280 155 HOH HOH . H 5 HOH H 59 281 156 HOH HOH . H 5 HOH H 60 282 157 HOH HOH . H 5 HOH H 61 283 161 HOH HOH . H 5 HOH H 62 284 163 HOH HOH . H 5 HOH H 63 285 164 HOH HOH . H 5 HOH H 64 286 170 HOH HOH . H 5 HOH H 65 287 172 HOH HOH . H 5 HOH H 66 288 174 HOH HOH . H 5 HOH H 67 289 177 HOH HOH . H 5 HOH H 68 290 180 HOH HOH . H 5 HOH H 69 291 181 HOH HOH . H 5 HOH H 70 292 184 HOH HOH . H 5 HOH H 71 293 187 HOH HOH . H 5 HOH H 72 294 189 HOH HOH . H 5 HOH H 73 295 190 HOH HOH . H 5 HOH H 74 296 195 HOH HOH . H 5 HOH H 75 297 197 HOH HOH . H 5 HOH H 76 298 198 HOH HOH . H 5 HOH H 77 299 203 HOH HOH . I 5 HOH C 1 204 5 HOH HOH . I 5 HOH C 2 205 9 HOH HOH . I 5 HOH C 3 206 30 HOH HOH . I 5 HOH C 4 207 39 HOH HOH . I 5 HOH C 5 208 41 HOH HOH . I 5 HOH C 6 209 50 HOH HOH . I 5 HOH C 7 210 59 HOH HOH . I 5 HOH C 8 211 67 HOH HOH . I 5 HOH C 9 212 68 HOH HOH . I 5 HOH C 10 213 71 HOH HOH . I 5 HOH C 11 214 76 HOH HOH . I 5 HOH C 12 215 81 HOH HOH . I 5 HOH C 13 216 83 HOH HOH . I 5 HOH C 14 217 85 HOH HOH . I 5 HOH C 15 218 86 HOH HOH . I 5 HOH C 16 219 106 HOH HOH . I 5 HOH C 17 220 107 HOH HOH . I 5 HOH C 18 221 116 HOH HOH . I 5 HOH C 19 222 119 HOH HOH . I 5 HOH C 20 223 121 HOH HOH . I 5 HOH C 21 224 125 HOH HOH . I 5 HOH C 22 225 133 HOH HOH . I 5 HOH C 23 226 137 HOH HOH . I 5 HOH C 24 227 139 HOH HOH . I 5 HOH C 25 228 141 HOH HOH . I 5 HOH C 26 229 145 HOH HOH . I 5 HOH C 27 230 146 HOH HOH . I 5 HOH C 28 231 151 HOH HOH . I 5 HOH C 29 232 152 HOH HOH . I 5 HOH C 30 233 160 HOH HOH . I 5 HOH C 31 234 166 HOH HOH . I 5 HOH C 32 235 168 HOH HOH . I 5 HOH C 33 236 175 HOH HOH . I 5 HOH C 34 237 179 HOH HOH . I 5 HOH C 35 238 194 HOH HOH . I 5 HOH C 36 239 196 HOH HOH . I 5 HOH C 37 240 199 HOH HOH . I 5 HOH C 38 241 201 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 . . . F 4 104.911 63.831 37.739 1 79.15 ? C1 NAG 203 C 1 HETATM 2 C C2 NAG . . . F 4 106.204 63.845 36.898 1 81.51 ? C2 NAG 203 C 1 HETATM 3 C C3 NAG . . . F 4 107.418 64.481 37.629 1 85.02 ? C3 NAG 203 C 1 HETATM 4 C C4 NAG . . . F 4 107.01 65.793 38.3 1 84.88 ? C4 NAG 203 C 1 HETATM 5 C C5 NAG . . . F 4 105.807 65.518 39.2 1 82.72 ? C5 NAG 203 C 1 HETATM 6 C C6 NAG . . . F 4 105.358 66.755 39.963 1 81.55 ? C6 NAG 203 C 1 HETATM 7 C C7 NAG . . . F 4 107.663 62.189 35.882 1 84.48 ? C7 NAG 203 C 1 HETATM 8 C C8 NAG . . . F 4 107.785 62.598 34.417 1 81.99 ? C8 NAG 203 C 1 HETATM 9 N N2 NAG . . . F 4 106.523 62.476 36.51 1 82.64 ? N2 NAG 203 C 1 HETATM 10 O O3 NAG . . . F 4 108.443 64.754 36.673 1 86.71 ? O3 NAG 203 C 1 HETATM 11 O O4 NAG . . . F 4 108.092 66.319 39.06 1 88.09 ? O4 NAG 203 C 1 HETATM 12 O O5 NAG . . . F 4 104.686 65.081 38.397 1 81.76 ? O5 NAG 203 C 1 HETATM 13 O O6 NAG . . . F 4 105.648 67.943 39.24 1 82.61 ? O6 NAG 203 C 1 HETATM 14 O O7 NAG . . . F 4 108.579 61.567 36.425 1 83.18 ? O7 NAG 203 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #