data_8VQ9 # _model_server_result.job_id Sm4YaXiLnDU8oCeBALxW2g _model_server_result.datetime_utc '2024-11-05 09:22:53' _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 8vq9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":1302}' # _entry.id 8VQ9 # _exptl.entry_id 8VQ9 _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_and_software_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,P,Q,R,S,T,U _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 x,y,z _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 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 T N N ? 3 U N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 1325 NAG 2 n D NAG 2 D 2 NAG A 1326 NAG 2 n E NAG 1 E 1 NAG A 1327 NAG 2 n E NAG 2 E 2 NAG A 1328 NAG 2 n F NAG 1 F 1 NAG A 1330 NAG 2 n F NAG 2 F 2 NAG A 1331 NAG 2 n G NAG 1 G 1 NAG B 1325 NAG 2 n G NAG 2 G 2 NAG B 1326 NAG 2 n H NAG 1 H 1 NAG B 1327 NAG 2 n H NAG 2 H 2 NAG B 1328 NAG 2 n I NAG 1 I 1 NAG B 1330 NAG 2 n I NAG 2 I 2 NAG B 1331 NAG 2 n J NAG 1 J 1 NAG C 1325 NAG 2 n J NAG 2 J 2 NAG C 1326 NAG 2 n K NAG 1 K 1 NAG C 1327 NAG 2 n K NAG 2 K 2 NAG C 1328 NAG 2 n L NAG 1 L 1 NAG C 1330 NAG 2 n L NAG 2 L 2 NAG C 1331 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 54 A CYS 707 1_555 C SG CYS 230 C CYS 883 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? disulf ? disulf2 A SG CYS 85 A CYS 738 1_555 A SG CYS 107 A CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf3 A SG CYS 90 A CYS 743 1_555 A SG CYS 96 A CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 187 A CYS 840 1_555 A SG CYS 198 A CYS 851 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 230 A CYS 883 1_555 B SG CYS 54 B CYS 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? disulf ? disulf6 A SG CYS 317 A CYS 970 1_555 A SG CYS 346 A CYS 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf7 A SG CYS 379 A CYS 1032 1_555 A SG CYS 390 A CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 A SG CYS 429 A CYS 1082 1_555 A SG CYS 473 A CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf9 B SG CYS 85 B CYS 738 1_555 B SG CYS 107 B CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf10 B SG CYS 90 B CYS 743 1_555 B SG CYS 96 B CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 187 B CYS 840 1_555 B SG CYS 198 B CYS 851 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 B SG CYS 230 B CYS 883 1_555 C SG CYS 54 C CYS 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? disulf ? disulf13 B SG CYS 317 B CYS 970 1_555 B SG CYS 346 B CYS 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf14 B SG CYS 379 B CYS 1032 1_555 B SG CYS 390 B CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf15 B SG CYS 429 B CYS 1082 1_555 B SG CYS 473 B CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf16 C SG CYS 85 C CYS 738 1_555 C SG CYS 107 C CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf17 C SG CYS 90 C CYS 743 1_555 C SG CYS 96 C CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf18 C SG CYS 187 C CYS 840 1_555 C SG CYS 198 C CYS 851 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf19 C SG CYS 317 C CYS 970 1_555 C SG CYS 346 C CYS 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf20 C SG CYS 379 C CYS 1032 1_555 C SG CYS 390 C CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf21 C SG CYS 429 C CYS 1082 1_555 C SG CYS 473 C CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 A ND2 ASN 56 A ASN 709 1_555 M C1 NAG . A NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale2 A ND2 ASN 64 A ASN 717 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? covale ? covale3 A ND2 ASN 148 A ASN 801 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale4 A ND2 ASN 421 A ASN 1074 1_555 N C1 NAG . A NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale5 A ND2 ASN 445 A ASN 1098 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale6 A ND2 ASN 481 A ASN 1134 1_555 O C1 NAG . A NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale7 B ND2 ASN 56 B ASN 709 1_555 P C1 NAG . B NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale8 B ND2 ASN 64 B ASN 717 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? covale ? covale9 B ND2 ASN 148 B ASN 801 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale10 B ND2 ASN 421 B ASN 1074 1_555 Q C1 NAG . B NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale11 B ND2 ASN 445 B ASN 1098 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale12 B ND2 ASN 481 B ASN 1134 1_555 R C1 NAG . B NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale13 C ND2 ASN 56 C ASN 709 1_555 S C1 NAG . C NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale14 C ND2 ASN 64 C ASN 717 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? covale ? covale15 C ND2 ASN 148 C ASN 801 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale16 C ND2 ASN 421 C ASN 1074 1_555 T C1 NAG . C NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale17 C ND2 ASN 445 C ASN 1098 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale18 C ND2 ASN 481 C ASN 1134 1_555 U C1 NAG . C NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale19 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale20 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale21 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale22 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? covale ? covale23 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale24 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale25 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? covale ? covale26 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale27 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? # _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 8VQ9 _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 M 3 NAG A 1 1301 1324 NAG NAG . N 3 NAG A 1 1302 1329 NAG NAG . O 3 NAG A 1 1303 1332 NAG NAG . P 3 NAG B 1 1301 1324 NAG NAG . Q 3 NAG B 1 1302 1329 NAG NAG . R 3 NAG B 1 1303 1332 NAG NAG . S 3 NAG C 1 1301 1324 NAG NAG . T 3 NAG C 1 1302 1329 NAG NAG . U 3 NAG C 1 1303 1332 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 . . . T 3 146.478 184.671 188.641 1 40.69 ? C1 NAG 1302 C 1 HETATM 2 C C2 NAG . . . T 3 145.255 183.803 188.194 1 40.91 ? C2 NAG 1302 C 1 HETATM 3 C C3 NAG . . . T 3 144.983 184.078 186.699 1 41.25 ? C3 NAG 1302 C 1 HETATM 4 C C4 NAG . . . T 3 144.709 185.582 186.502 1 41.39 ? C4 NAG 1302 C 1 HETATM 5 C C5 NAG . . . T 3 145.938 186.376 187.001 1 41.24 ? C5 NAG 1302 C 1 HETATM 6 C C6 NAG . . . T 3 145.734 187.877 186.886 1 41.43 ? C6 NAG 1302 C 1 HETATM 7 C C7 NAG . . . T 3 145.129 181.705 189.41 1 40.36 ? C7 NAG 1302 C 1 HETATM 8 C C8 NAG . . . T 3 145.477 180.258 189.565 1 39.65 ? C8 NAG 1302 C 1 HETATM 9 N N2 NAG . . . T 3 145.584 182.385 188.366 1 40.62 ? N2 NAG 1302 C 1 HETATM 10 O O3 NAG . . . T 3 143.847 183.317 186.273 1 41.37 ? O3 NAG 1302 C 1 HETATM 11 O O4 NAG . . . T 3 144.481 185.841 185.12 1 41.46 ? O4 NAG 1302 C 1 HETATM 12 O O5 NAG . . . T 3 146.197 186.067 188.408 1 40.77 ? O5 NAG 1302 C 1 HETATM 13 O O6 NAG . . . T 3 144.551 188.302 187.55 1 41.86 ? O6 NAG 1302 C 1 HETATM 14 O O7 NAG . . . T 3 144.404 182.253 190.245 1 40.67 ? O7 NAG 1302 C 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 209 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #