data_8DG8 # _model_server_result.job_id atOcFpxkE81v7NCh9o1SDw _model_server_result.datetime_utc '2024-11-29 07:29:10' _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 8dg8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":602}' # _entry.id 8DG8 # _exptl.entry_id 8DG8 _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 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8DG8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DG8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N 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 45 B CYS 63 1_555 A SG CYS 174 B CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 144 B CYS 162 1_555 A SG CYS 150 B CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 195 B CYS 213 1_555 A SG CYS 212 B CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 A SG CYS 313 B CYS 331 1_555 A SG CYS 322 B CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 337 B CYS 355 1_555 A SG CYS 345 B CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 369 B CYS 387 1_555 A SG CYS 374 B CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 376 B CYS 394 1_555 A SG CYS 399 B CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 C SG CYS 22 L CYS 23 1_555 C SG CYS 87 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 D SG CYS 45 A CYS 63 1_555 D SG CYS 174 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 D SG CYS 144 A CYS 162 1_555 D SG CYS 150 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 D SG CYS 195 A CYS 213 1_555 D SG CYS 212 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 D SG CYS 313 A CYS 331 1_555 D SG CYS 322 A CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf14 D SG CYS 337 A CYS 355 1_555 D SG CYS 345 A CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf15 D SG CYS 369 A CYS 387 1_555 D SG CYS 374 A CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf16 D SG CYS 376 A CYS 394 1_555 D SG CYS 399 A CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 E SG CYS 45 C CYS 63 1_555 E SG CYS 174 C CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 E SG CYS 144 C CYS 162 1_555 E SG CYS 150 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf19 E SG CYS 195 C CYS 213 1_555 E SG CYS 212 C CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf20 E SG CYS 313 C CYS 331 1_555 E SG CYS 322 C CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf21 E SG CYS 337 C CYS 355 1_555 E SG CYS 345 C CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf22 E SG CYS 369 C CYS 387 1_555 E SG CYS 374 C CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf23 E SG CYS 376 C CYS 394 1_555 E SG CYS 399 C CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 220 B ASN 238 1_555 F C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 341 B ASN 359 1_555 G C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale3 A ND2 ASN 428 B ASN 446 1_555 H C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 D ND2 ASN 220 A ASN 238 1_555 I C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 D ND2 ASN 341 A ASN 359 1_555 J C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 D ND2 ASN 428 A ASN 446 1_555 K C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 E ND2 ASN 220 C ASN 238 1_555 L C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 E ND2 ASN 341 C ASN 359 1_555 M C1 NAG . C NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale9 E ND2 ASN 428 C ASN 446 1_555 N C1 NAG . C NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _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 8DG8 _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 F 4 NAG B 1 601 473 NAG NAG . G 4 NAG B 1 602 474 NAG NAG . H 4 NAG B 1 603 475 NAG NAG . I 4 NAG A 1 601 473 NAG NAG . J 4 NAG A 1 602 474 NAG NAG . K 4 NAG A 1 603 475 NAG NAG . L 4 NAG C 1 601 473 NAG NAG . M 4 NAG C 1 602 474 NAG NAG . N 4 NAG C 1 603 475 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 . . . J 4 183.857 178.032 217.152 1 119.28 ? C1 NAG 602 A 1 HETATM 2 C C2 NAG . . . J 4 182.922 176.93 217.69 1 119.28 ? C2 NAG 602 A 1 HETATM 3 C C3 NAG . . . J 4 182.884 176.946 219.217 1 119.28 ? C3 NAG 602 A 1 HETATM 4 C C4 NAG . . . J 4 184.29 176.933 219.801 1 119.28 ? C4 NAG 602 A 1 HETATM 5 C C5 NAG . . . J 4 185.13 178.049 219.19 1 119.28 ? C5 NAG 602 A 1 HETATM 6 C C6 NAG . . . J 4 186.565 178.036 219.668 1 119.28 ? C6 NAG 602 A 1 HETATM 7 C C7 NAG . . . J 4 180.756 178.079 217.383 1 119.28 ? C7 NAG 602 A 1 HETATM 8 C C8 NAG . . . J 4 179.415 178.012 216.722 1 119.28 ? C8 NAG 602 A 1 HETATM 9 N N2 NAG . . . J 4 181.58 177.052 217.137 1 119.28 ? N2 NAG 602 A 1 HETATM 10 O O3 NAG . . . J 4 182.16 175.812 219.678 1 119.28 ? O3 NAG 602 A 1 HETATM 11 O O4 NAG . . . J 4 184.227 177.112 221.212 1 119.28 ? O4 NAG 602 A 1 HETATM 12 O O5 NAG . . . J 4 185.156 177.908 217.761 1 119.28 ? O5 NAG 602 A 1 HETATM 13 O O6 NAG . . . J 4 187.47 177.801 218.599 1 119.28 ? O6 NAG 602 A 1 HETATM 14 O O7 NAG . . . J 4 181.079 179.023 218.102 1 119.28 ? O7 NAG 602 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #