data_8PK3 # _model_server_result.job_id qa4UdM22R8POr_Hnv7QwIw _model_server_result.datetime_utc '2025-02-28 04:48:37' _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 8pk3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":401}' # _entry.id 8PK3 # _exptl.entry_id 8PK3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8PK3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PK3 _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,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 ? _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 ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T N N ? 6 U N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 5 5 3 MAN BMA C1 O1 . O6 HO6 . 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 4 n J NAG 1 J 1 NAG A 329 NAG 4 n J NAG 2 J 2 NAG A 330 NAG 5 n K NAG 1 N 1 NAG A 333 NAG 5 n K NAG 2 N 2 NAG A 334 NAG 5 n K BMA 3 N 3 BMA A 335 BMA 5 n K MAN 4 N 4 MAN A 336 MAN 5 n K MAN 5 N 5 MAN A 337 MAN 4 n L NAG 1 S 1 NAG B 329 NAG 4 n L NAG 2 S 2 NAG B 330 NAG 5 n M NAG 1 W 1 NAG B 333 NAG 5 n M NAG 2 W 2 NAG B 334 NAG 5 n M BMA 3 W 3 BMA B 335 BMA 5 n M MAN 4 W 4 MAN B 336 MAN 5 n M MAN 5 W 5 MAN B 337 MAN 4 n N NAG 1 b 1 NAG C 329 NAG 4 n N NAG 2 b 2 NAG C 330 NAG 5 n O NAG 1 f 1 NAG C 333 NAG 5 n O NAG 2 f 2 NAG C 334 NAG 5 n O BMA 3 f 3 BMA C 335 BMA 5 n O MAN 4 f 4 MAN C 336 MAN 5 n O MAN 5 f 5 MAN C 337 MAN # 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 8 A CYS 14 1_555 B SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 271 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 58 A CYS 64 1_555 A SG CYS 70 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 91 A CYS 97 1_555 A SG CYS 133 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 A SG CYS 275 A CYS 281 1_555 A SG CYS 299 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf6 B SG CYS 144 D CYS 144 1_555 B SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 D SG CYS 8 B CYS 14 1_555 E SG CYS 137 E CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 D SG CYS 46 B CYS 52 1_555 D SG CYS 271 B CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 D SG CYS 58 B CYS 64 1_555 D SG CYS 70 B CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf10 D SG CYS 91 B CYS 97 1_555 D SG CYS 133 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 D SG CYS 275 B CYS 281 1_555 D SG CYS 299 B CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf12 E SG CYS 144 E CYS 144 1_555 E SG CYS 148 E CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf13 G SG CYS 8 C CYS 14 1_555 H SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf14 G SG CYS 46 C CYS 52 1_555 G SG CYS 271 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 G SG CYS 58 C CYS 64 1_555 G SG CYS 70 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf16 G SG CYS 91 C CYS 97 1_555 G SG CYS 133 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf17 G SG CYS 275 C CYS 281 1_555 G SG CYS 299 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf18 H SG CYS 144 F CYS 144 1_555 H SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A ND2 ASN 32 A ASN 38 1_555 Q C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 75 A ASN 81 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A ND2 ASN 159 A ASN 165 1_555 K C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 A ND2 ASN 279 A ASN 285 1_555 P C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 D ND2 ASN 32 B ASN 38 1_555 S C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 D ND2 ASN 75 B ASN 81 1_555 L C1 NAG . S NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 D ND2 ASN 159 B ASN 165 1_555 M C1 NAG . W NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale8 D ND2 ASN 279 B ASN 285 1_555 R C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale9 G ND2 ASN 32 C ASN 38 1_555 U C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 G ND2 ASN 75 C ASN 81 1_555 N C1 NAG . b NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 G ND2 ASN 159 C ASN 165 1_555 O C1 NAG . f NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale12 G ND2 ASN 279 C ASN 285 1_555 T C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale14 K O4 NAG . N NAG 1 1_555 K C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale15 K O4 NAG . N NAG 2 1_555 K C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale16 K O3 BMA . N BMA 3 1_555 K C1 MAN . N MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale17 K O6 BMA . N BMA 3 1_555 K C1 MAN . N MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 L O4 NAG . S NAG 1 1_555 L C1 NAG . S NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale19 M O4 NAG . W NAG 1 1_555 M C1 NAG . W NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale20 M O4 NAG . W NAG 2 1_555 M C1 BMA . W BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale21 M O3 BMA . W BMA 3 1_555 M C1 MAN . W MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale22 M O6 BMA . W BMA 3 1_555 M C1 MAN . W MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale23 N O4 NAG . b NAG 1 1_555 N C1 NAG . b NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale24 O O4 NAG . f NAG 1 1_555 O C1 NAG . f NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale25 O O4 NAG . f NAG 2 1_555 O C1 BMA . f BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale26 O O3 BMA . f BMA 3 1_555 O C1 MAN . f MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale27 O O6 BMA . f BMA 3 1_555 O C1 MAN . f MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 8PK3 _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 P 6 NAG A 1 401 331 NAG NAG . Q 6 NAG A 1 402 332 NAG NAG . R 6 NAG B 1 401 331 NAG NAG . S 6 NAG B 1 402 332 NAG NAG . T 6 NAG C 1 401 331 NAG NAG . U 6 NAG C 1 402 332 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 . . . R 6 178.896 146.951 175.709 1 52.96 ? C1 NAG 401 B 1 HETATM 2 C C2 NAG . . . R 6 179.89 147.514 176.734 1 52.96 ? C2 NAG 401 B 1 HETATM 3 C C3 NAG . . . R 6 180.276 148.95 176.378 1 52.96 ? C3 NAG 401 B 1 HETATM 4 C C4 NAG . . . R 6 180.748 149.045 174.934 1 52.96 ? C4 NAG 401 B 1 HETATM 5 C C5 NAG . . . R 6 179.686 148.474 174.007 1 52.96 ? C5 NAG 401 B 1 HETATM 6 C C6 NAG . . . R 6 180.114 148.457 172.56 1 52.96 ? C6 NAG 401 B 1 HETATM 7 C C7 NAG . . . R 6 180.069 147.399 179.182 1 52.96 ? C7 NAG 401 B 1 HETATM 8 C C8 NAG . . . R 6 179.315 147.35 180.475 1 52.96 ? C8 NAG 401 B 1 HETATM 9 N N2 NAG . . . R 6 179.326 147.458 178.073 1 52.96 ? N2 NAG 401 B 1 HETATM 10 O O3 NAG . . . R 6 181.311 149.394 177.246 1 52.96 ? O3 NAG 401 B 1 HETATM 11 O O4 NAG . . . R 6 180.992 150.402 174.584 1 52.96 ? O4 NAG 401 B 1 HETATM 12 O O5 NAG . . . R 6 179.422 147.114 174.379 1 52.96 ? O5 NAG 401 B 1 HETATM 13 O O6 NAG . . . R 6 179.182 149.141 171.734 1 52.96 ? O6 NAG 401 B 1 HETATM 14 O O7 NAG . . . R 6 181.295 147.389 179.144 1 52.96 ? O7 NAG 401 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #