data_8DMK # _model_server_result.job_id 6FXhhoK2uaWb-zGee-0FkA _model_server_result.datetime_utc '2025-07-05 13:13:33' _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 8dmk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 8DMK # _exptl.entry_id 8DMK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 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 ? 4 F N N ? 4 G N N ? 4 H 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 21 A CYS 48 1_555 A SG CYS 49 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 30 A CYS 57 1_555 A SG CYS 46 A CYS 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 139 A CYS 166 1_555 A SG CYS 162 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 250 A CYS 277 1_555 A SG CYS 259 A CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 252 A CYS 279 1_555 A SG CYS 270 A CYS 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 272 A CYS 299 1_555 A SG CYS 281 A CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 277 A CYS 304 1_555 A SG CYS 285 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 A SG CYS 284 A CYS 311 1_555 A SG CYS 304 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 2 B CYS 30 1_555 B SG CYS 7 B CYS 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 B SG CYS 28 B CYS 56 1_555 B SG CYS 51 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 37 B CYS 65 1_555 B SG CYS 48 B CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 B SG CYS 142 B CYS 170 1_555 B SG CYS 162 B CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 B SG CYS 243 B CYS 271 1_555 B SG CYS 252 B CYS 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf14 B SG CYS 245 B CYS 273 1_555 B SG CYS 270 B CYS 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 B SG CYS 272 B CYS 300 1_555 B SG CYS 281 B CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 B SG CYS 284 B CYS 312 1_555 B SG CYS 304 B CYS 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 C SG CYS 33 G CYS 69 1_555 C SG CYS 56 G CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf18 C SG CYS 41 G CYS 77 1_555 C SG CYS 53 G CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf19 C SG CYS 146 G CYS 182 1_555 C SG CYS 169 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf20 C SG CYS 250 G CYS 286 1_555 C SG CYS 259 G CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 C SG CYS 252 G CYS 288 1_555 C SG CYS 269 G CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf22 C SG CYS 271 G CYS 307 1_555 C SG CYS 280 G CYS 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf23 C SG CYS 283 G CYS 319 1_555 C SG CYS 303 G CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 18 A ASN 45 1_555 D C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 52 A ASN 79 1_555 E C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 B ND2 ASN 92 B ASN 120 1_555 F C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 C ND2 ASN 24 G ASN 60 1_555 G C1 NAG . G NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 C O PHE 69 G PHE 105 1_555 I CA CA . G CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc2 C OD1 ASP 72 G ASP 108 1_555 I CA CA . G CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc3 C OD2 ASP 72 G ASP 108 1_555 I CA CA . G CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc4 C O THR 80 G THR 116 1_555 I CA CA . G CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc5 C OG1 THR 80 G THR 116 1_555 I CA CA . G CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc6 C O SER 242 G SER 278 1_555 I CA CA . G CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 8DMK _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 1 401 333 NAG NAG . E 4 NAG A 1 402 334 NAG NAG . F 4 NAG B 1 401 336 NAG NAG . G 4 NAG G 1 401 342 NAG NAG . H 4 NAG G 1 402 343 NAG NAG . I 5 CA G 1 403 344 CA CA . # 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 . . . E 4 167.385 120.892 130.989 1 50 ? C1 NAG 402 A 1 HETATM 2 C C2 NAG . . . E 4 168.86 120.473 130.934 1 50 ? C2 NAG 402 A 1 HETATM 3 C C3 NAG . . . E 4 168.986 118.962 131.106 1 50 ? C3 NAG 402 A 1 HETATM 4 C C4 NAG . . . E 4 168.266 118.506 132.368 1 50 ? C4 NAG 402 A 1 HETATM 5 C C5 NAG . . . E 4 166.821 118.998 132.36 1 50 ? C5 NAG 402 A 1 HETATM 6 C C6 NAG . . . E 4 166.077 118.673 133.635 1 50 ? C6 NAG 402 A 1 HETATM 7 C C7 NAG . . . E 4 170.612 121.608 129.637 1 50 ? C7 NAG 402 A 1 HETATM 8 C C8 NAG . . . E 4 171.234 121.956 130.957 1 50 ? C8 NAG 402 A 1 HETATM 9 N N2 NAG . . . E 4 169.479 120.9 129.689 1 50 ? N2 NAG 402 A 1 HETATM 10 O O3 NAG . . . E 4 170.362 118.607 131.174 1 50 ? O3 NAG 402 A 1 HETATM 11 O O4 NAG . . . E 4 168.277 117.085 132.45 1 50 ? O4 NAG 402 A 1 HETATM 12 O O5 NAG . . . E 4 166.794 120.425 132.218 1 50 ? O5 NAG 402 A 1 HETATM 13 O O6 NAG . . . E 4 164.804 119.302 133.668 1 50 ? O6 NAG 402 A 1 HETATM 14 O O7 NAG . . . E 4 171.113 121.954 128.572 1 50 ? O7 NAG 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #