data_6JK8 # _model_server_result.job_id tzziPUAluOHmdenK2OehZw _model_server_result.datetime_utc '2024-11-29 17:20:01' _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 6jk8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1404}' # _entry.id 6JK8 # _exptl.entry_id 6JK8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 ? 5 J N N ? 5 K N N ? 5 L N N ? 5 M N N ? 5 N N N ? 5 O N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 MAN MAN 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 3 n E NAG 1 E 1 NAG A 1402 NAG 3 n E NAG 2 E 2 NAG A 1403 NAG 4 n F NAG 1 F 1 NAG A 1405 NAG 4 n F NAG 2 F 2 NAG A 1406 NAG 4 n F MAN 3 F 3 MAN A 1407 MAN 4 n F MAN 4 F 4 MAN A 1408 MAN 3 n G NAG 1 G 1 NAG A 1410 NAG 3 n G NAG 2 G 2 NAG A 1411 NAG 3 n H NAG 1 H 1 NAG B 1402 NAG 3 n H NAG 2 H 2 NAG B 1403 NAG 3 n I NAG 1 I 1 NAG B 1405 NAG 3 n I NAG 2 I 2 NAG B 1406 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 33 A CYS 33 1_555 A SG CYS 52 A CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf2 A SG CYS 150 A CYS 150 1_555 A SG CYS 178 A CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 182 A CYS 182 1_555 A SG CYS 205 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 A SG CYS 192 A CYS 192 1_555 A SG CYS 211 A CYS 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 215 A CYS 215 1_555 A SG CYS 224 A CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 219 A CYS 219 1_555 A SG CYS 230 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 A SG CYS 231 A CYS 231 1_555 A SG CYS 239 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf8 A SG CYS 235 A CYS 235 1_555 A SG CYS 248 A CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 A SG CYS 251 A CYS 251 1_555 A SG CYS 260 A CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 A SG CYS 264 A CYS 264 1_555 A SG CYS 276 A CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 A SG CYS 282 A CYS 282 1_555 A SG CYS 303 A CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf12 A SG CYS 307 A CYS 307 1_555 A SG CYS 321 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf13 A SG CYS 332 A CYS 332 1_555 A SG CYS 353 A CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf14 A SG CYS 663 A CYS 663 1_555 A SG CYS 879 A CYS 880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 A SG CYS 699 A CYS 700 1_555 A SG CYS 702 A CYS 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf16 A SG CYS 806 A CYS 807 1_555 A SG CYS 815 A CYS 816 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf17 B SG CYS 33 B CYS 33 1_555 B SG CYS 52 B CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf18 B SG CYS 150 B CYS 150 1_555 B SG CYS 178 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf19 B SG CYS 182 B CYS 182 1_555 B SG CYS 205 B CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf20 B SG CYS 192 B CYS 192 1_555 B SG CYS 211 B CYS 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf21 B SG CYS 215 B CYS 215 1_555 B SG CYS 224 B CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf22 B SG CYS 219 B CYS 219 1_555 B SG CYS 230 B CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf23 B SG CYS 231 B CYS 231 1_555 B SG CYS 239 B CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf24 B SG CYS 235 B CYS 235 1_555 B SG CYS 248 B CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? disulf ? disulf25 B SG CYS 251 B CYS 251 1_555 B SG CYS 260 B CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf26 B SG CYS 264 B CYS 264 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf27 B SG CYS 282 B CYS 282 1_555 B SG CYS 303 B CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf28 B SG CYS 307 B CYS 307 1_555 B SG CYS 321 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf29 B SG CYS 332 B CYS 332 1_555 B SG CYS 353 B CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf30 B SG CYS 663 B CYS 663 1_555 B SG CYS 879 B CYS 880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf31 B SG CYS 806 B CYS 807 1_555 B SG CYS 815 B CYS 816 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf32 C SG CYS 95 C CYS 6 1_555 C SG CYS 100 C CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf33 C SG CYS 96 C CYS 7 1_555 D SG CYS 31 D CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf34 C SG CYS 109 C CYS 20 1_555 D SG CYS 43 D CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? covale ? covale1 A ND2 ASN 51 A ASN 51 1_555 J C1 NAG . A NAG 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 135 A ASN 135 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 A ND2 ASN 534 A ASN 534 1_555 K C1 NAG . A NAG 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale4 A ND2 ASN 607 A ASN 607 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale5 A ND2 ASN 900 A ASN 901 1_555 L C1 NAG . A NAG 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale6 A ND2 ASN 913 A ASN 914 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 B ND2 ASN 51 B ASN 51 1_555 M C1 NAG . B NAG 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 B ND2 ASN 135 B ASN 135 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 B ND2 ASN 534 B ASN 534 1_555 N C1 NAG . B NAG 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 B ND2 ASN 607 B ASN 607 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale13 F O4 NAG . F NAG 2 1_555 F C1 MAN . F MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.489 ? covale ? covale14 F O4 MAN . F MAN 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale15 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale17 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 6JK8 _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 J 5 NAG A 1 1401 1401 NAG NAG . K 5 NAG A 1 1404 1404 NAG NAG . L 5 NAG A 1 1409 1409 NAG NAG . M 5 NAG B 1 1401 1401 NAG NAG . N 5 NAG B 1 1404 1404 NAG NAG . O 5 NAG B 1 1407 1407 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 . . . N 5 95.918 83.879 109.648 1 225.18 ? C1 NAG 1404 B 1 HETATM 2 C C2 NAG . . . N 5 97.381 84.187 109.776 1 225.18 ? C2 NAG 1404 B 1 HETATM 3 C C3 NAG . . . N 5 97.805 84.998 108.574 1 225.18 ? C3 NAG 1404 B 1 HETATM 4 C C4 NAG . . . N 5 97.577 84.18 107.309 1 225.18 ? C4 NAG 1404 B 1 HETATM 5 C C5 NAG . . . N 5 96.163 83.567 107.249 1 225.18 ? C5 NAG 1404 B 1 HETATM 6 C C6 NAG . . . N 5 96.062 82.447 106.243 1 225.18 ? C6 NAG 1404 B 1 HETATM 7 C C7 NAG . . . N 5 98.162 84.288 112.094 1 225.18 ? C7 NAG 1404 B 1 HETATM 8 C C8 NAG . . . N 5 98.435 85.168 113.273 1 225.18 ? C8 NAG 1404 B 1 HETATM 9 N N2 NAG . . . N 5 97.68 84.897 111.006 1 225.18 ? N2 NAG 1404 B 1 HETATM 10 O O3 NAG . . . N 5 99.18 85.34 108.692 1 225.18 ? O3 NAG 1404 B 1 HETATM 11 O O4 NAG . . . N 5 97.759 85.019 106.174 1 225.18 ? O4 NAG 1404 B 1 HETATM 12 O O5 NAG . . . N 5 95.713 83.029 108.514 1 225.18 ? O5 NAG 1404 B 1 HETATM 13 O O6 NAG . . . N 5 97.154 82.475 105.336 1 225.18 ? O6 NAG 1404 B 1 HETATM 14 O O7 NAG . . . N 5 98.359 83.077 112.128 1 225.18 ? O7 NAG 1404 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 42 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 580 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #