data_8YG6 # _model_server_result.job_id 2SyeC-4NQNS6TGHs9lLGqQ _model_server_result.datetime_utc '2024-10-10 00:26:46' _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 8yg6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":501}' # _entry.id 8YG6 # _exptl.entry_id 8YG6 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 9 _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,J,K,L,M,N,O _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 ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NAG NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n D NAG 1 D 1 NAG A 1354 NAG 2 n D NAG 2 D 2 NAG A 1355 NAG 2 n D NAG 3 D 3 NAG A 1356 NAG 2 n E NAG 1 E 1 NAG B 1354 NAG 2 n E NAG 2 E 2 NAG B 1355 NAG 2 n E NAG 3 E 3 NAG B 1356 NAG 2 n F NAG 1 F 1 NAG C 1354 NAG 2 n F NAG 2 F 2 NAG C 1355 NAG 2 n F NAG 3 F 3 NAG C 1356 NAG # 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 2 A CYS 24 1_555 B SG CYS 350 B CYS 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? disulf ? disulf2 A SG CYS 89 A CYS 111 1_555 A SG CYS 142 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 106 A CYS 128 1_555 A SG CYS 136 A CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 155 A CYS 177 1_555 A SG CYS 162 A CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 206 A CYS 228 1_555 A SG CYS 224 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 240 A CYS 262 1_555 A SG CYS 245 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 A SG CYS 350 A CYS 372 1_555 C SG CYS 2 C CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? disulf ? disulf8 A SG CYS 360 A CYS 382 1_555 A SG CYS 380 A CYS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 2 B CYS 24 1_555 C SG CYS 350 C CYS 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? disulf ? disulf10 B SG CYS 89 B CYS 111 1_555 B SG CYS 142 B CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf11 B SG CYS 106 B CYS 128 1_555 B SG CYS 136 B CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 B SG CYS 155 B CYS 177 1_555 B SG CYS 162 B CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 B SG CYS 206 B CYS 228 1_555 B SG CYS 224 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf14 B SG CYS 240 B CYS 262 1_555 B SG CYS 245 B CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf15 B SG CYS 360 B CYS 382 1_555 B SG CYS 380 B CYS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 C SG CYS 89 C CYS 111 1_555 C SG CYS 142 C CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf17 C SG CYS 106 C CYS 128 1_555 C SG CYS 136 C CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf18 C SG CYS 155 C CYS 177 1_555 C SG CYS 162 C CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 C SG CYS 206 C CYS 228 1_555 C SG CYS 224 C CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf20 C SG CYS 240 C CYS 262 1_555 C SG CYS 245 C CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf21 C SG CYS 360 C CYS 382 1_555 C SG CYS 380 C CYS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 175 A ASN 197 1_555 G C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 332 A ASN 354 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 362 A ASN 384 1_555 H C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 A ND2 ASN 404 A ASN 426 1_555 I C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 175 B ASN 197 1_555 J C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 B ND2 ASN 332 B ASN 354 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B ND2 ASN 362 B ASN 384 1_555 K C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 B ND2 ASN 404 B ASN 426 1_555 L C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 C ND2 ASN 175 C ASN 197 1_555 M C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 C ND2 ASN 332 C ASN 354 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 C ND2 ASN 362 C ASN 384 1_555 N C1 NAG . C NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 C ND2 ASN 404 C ASN 426 1_555 O C1 NAG . C NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale14 D O4 NAG . D NAG 2 1_555 D C1 NAG . D NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale15 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 E O4 NAG . E NAG 2 1_555 E C1 NAG . E NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 F O4 NAG . F NAG 2 1_555 F C1 NAG . F NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _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 8YG6 _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 G 3 NAG A 1 501 1197 NAG NAG . H 3 NAG A 1 502 1384 NAG NAG . I 3 NAG A 1 503 1426 NAG NAG . J 3 NAG B 1 501 1197 NAG NAG . K 3 NAG B 1 502 1384 NAG NAG . L 3 NAG B 1 503 1426 NAG NAG . M 3 NAG C 1 501 1197 NAG NAG . N 3 NAG C 1 502 1384 NAG NAG . O 3 NAG C 1 503 1426 NAG NAG . # 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 . . . M 3 128.627 174.846 146.387 1 157.95 ? C1 NAG 501 C 1 HETATM 2 C C2 NAG . . . M 3 128.566 173.326 146.204 1 157.95 ? C2 NAG 501 C 1 HETATM 3 C C3 NAG . . . M 3 127.871 172.98 144.891 1 157.95 ? C3 NAG 501 C 1 HETATM 4 C C4 NAG . . . M 3 126.513 173.663 144.807 1 157.95 ? C4 NAG 501 C 1 HETATM 5 C C5 NAG . . . M 3 126.66 175.163 145.045 1 157.95 ? C5 NAG 501 C 1 HETATM 6 C C6 NAG . . . M 3 125.336 175.889 145.093 1 157.95 ? C6 NAG 501 C 1 HETATM 7 C C7 NAG . . . M 3 130.207 171.688 147.016 1 157.95 ? C7 NAG 501 C 1 HETATM 8 C C8 NAG . . . M 3 129.095 171.127 147.852 1 157.95 ? C8 NAG 501 C 1 HETATM 9 N N2 NAG . . . M 3 129.895 172.738 146.251 1 157.95 ? N2 NAG 501 C 1 HETATM 10 O O3 NAG . . . M 3 127.71 171.569 144.801 1 157.95 ? O3 NAG 501 C 1 HETATM 11 O O4 NAG . . . M 3 125.938 173.449 143.523 1 157.95 ? O4 NAG 501 C 1 HETATM 12 O O5 NAG . . . M 3 127.304 175.394 146.306 1 157.95 ? O5 NAG 501 C 1 HETATM 13 O O6 NAG . . . M 3 125.164 176.575 146.325 1 157.95 ? O6 NAG 501 C 1 HETATM 14 O O7 NAG . . . M 3 131.339 171.211 147.035 1 157.95 ? O7 NAG 501 C 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #