data_8GC3 # _model_server_result.job_id xdQ7QCaEBBfFzoVOAXmNXw _model_server_result.datetime_utc '2024-10-19 13:27:07' _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 8gc3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":1002}' # _entry.id 8GC3 # _exptl.entry_id 8GC3 _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 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 8GC3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GC3 _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 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,P,Q,R,S,T,U,V _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 M N N ? 4 O N N ? 4 P N N ? 4 R N N ? 4 T N N ? 4 U N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 3 2 1 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 E NAG 1 E 1 NAG A 840 NAG 2 n E NAG 2 E 2 NAG A 841 NAG 2 n E BMA 3 E 3 BMA A 842 BMA 2 n E MAN 4 E 4 MAN A 843 MAN 2 n E MAN 5 E 5 MAN A 844 MAN 3 n F NAG 1 F 1 NAG A 846 NAG 3 n F NAG 2 F 2 NAG A 847 NAG 2 n G NAG 1 G 1 NAG A 848 NAG 2 n G NAG 2 G 2 NAG A 849 NAG 2 n G BMA 3 G 3 BMA A 850 BMA 2 n G MAN 4 G 4 MAN A 851 MAN 2 n G MAN 5 G 5 MAN A 852 MAN 2 n H NAG 1 H 1 NAG B 840 NAG 2 n H NAG 2 H 2 NAG B 841 NAG 2 n H BMA 3 H 3 BMA B 842 BMA 2 n H MAN 4 H 4 MAN B 843 MAN 2 n H MAN 5 H 5 MAN B 844 MAN 2 n I NAG 1 I 1 NAG C 840 NAG 2 n I NAG 2 I 2 NAG C 841 NAG 2 n I BMA 3 I 3 BMA C 842 BMA 2 n I MAN 4 I 4 MAN C 843 MAN 2 n I MAN 5 I 5 MAN C 844 MAN 3 n J NAG 1 J 1 NAG C 845 NAG 3 n J NAG 2 J 2 NAG C 846 NAG 2 n K NAG 1 K 1 NAG C 847 NAG 2 n K NAG 2 K 2 NAG C 848 NAG 2 n K BMA 3 K 3 BMA C 849 BMA 2 n K MAN 4 K 4 MAN C 850 MAN 2 n K MAN 5 K 5 MAN C 851 MAN 2 n L NAG 1 L 1 NAG D 840 NAG 2 n L NAG 2 L 2 NAG D 841 NAG 2 n L BMA 3 L 3 BMA D 842 BMA 2 n L MAN 4 L 4 MAN D 843 MAN 2 n L MAN 5 L 5 MAN D 844 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 63 A CYS 96 1_555 A SG CYS 314 A CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 63 B CYS 96 1_555 B SG CYS 314 B CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 C SG CYS 63 C CYS 96 1_555 C SG CYS 314 C CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 D SG CYS 63 D CYS 96 1_555 D SG CYS 314 D CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 242 A ASN 275 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale2 A ND2 ASN 345 A ASN 378 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 379 A ASN 412 1_555 M C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 397 A ASN 430 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale5 B ND2 ASN 242 B ASN 275 1_555 P C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 348 B ASN 381 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale7 B ND2 ASN 379 B ASN 412 1_555 O C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 C ND2 ASN 242 C ASN 275 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale9 C ND2 ASN 345 C ASN 378 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale10 C ND2 ASN 379 C ASN 412 1_555 R C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 C ND2 ASN 397 C ASN 430 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 D ND2 ASN 242 D ASN 275 1_555 U C1 NAG . D NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale13 D ND2 ASN 345 D ASN 378 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale14 D ND2 ASN 379 D ASN 412 1_555 T C1 NAG . D NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale15 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale16 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale17 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale18 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale19 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale20 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale21 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale22 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale23 G O6 BMA . G BMA 3 1_555 G C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.486 ? covale ? covale24 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale25 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale26 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? covale ? covale27 H O6 BMA . H BMA 3 1_555 H C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale28 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale29 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale30 I O3 BMA . I BMA 3 1_555 I C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale31 I O6 BMA . I BMA 3 1_555 I C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale32 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale33 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale34 K O4 NAG . K NAG 2 1_555 K C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale35 K O3 BMA . K BMA 3 1_555 K C1 MAN . K MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? covale ? covale36 K O6 BMA . K BMA 3 1_555 K C1 MAN . K MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.488 ? covale ? covale37 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale38 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale39 L O3 BMA . L BMA 3 1_555 L C1 MAN . L MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? covale ? covale40 L O6 BMA . L BMA 3 1_555 L C1 MAN . L MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? # _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 326 n n C1 O1 NAG sing 327 n n C1 O5 NAG sing 328 n n C1 H1 NAG sing 329 n n C2 C3 NAG sing 330 n n C2 N2 NAG sing 331 n n C2 H2 NAG sing 332 n n C3 C4 NAG sing 333 n n C3 O3 NAG sing 334 n n C3 H3 NAG sing 335 n n C4 C5 NAG sing 336 n n C4 O4 NAG sing 337 n n C4 H4 NAG sing 338 n n C5 C6 NAG sing 339 n n C5 O5 NAG sing 340 n n C5 H5 NAG sing 341 n n C6 O6 NAG sing 342 n n C6 H61 NAG sing 343 n n C6 H62 NAG sing 344 n n C7 C8 NAG sing 345 n n C7 N2 NAG sing 346 n n C7 O7 NAG doub 347 n n C8 H81 NAG sing 348 n n C8 H82 NAG sing 349 n n C8 H83 NAG sing 350 n n N2 HN2 NAG sing 351 n n O1 HO1 NAG sing 352 n n O3 HO3 NAG sing 353 n n O4 HO4 NAG sing 354 n n O6 HO6 NAG sing 355 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 8GC3 _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 4 NAG A 1 1001 845 NAG NAG . N 5 DOQ A 1 1002 901 DOQ DOQ . O 4 NAG B 1 1001 845 NAG NAG . P 4 NAG B 1 1002 846 NAG NAG . Q 5 DOQ B 1 1003 901 DOQ DOQ . R 4 NAG C 1 1001 852 NAG NAG . S 5 DOQ C 1 1002 901 DOQ DOQ . T 4 NAG D 1 1001 846 NAG NAG . U 4 NAG D 1 1002 847 NAG NAG . V 5 DOQ D 1 1003 901 DOQ DOQ . # 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 . . . U 4 215.812 219.94 275.935 1 121.07 ? C1 NAG 1002 D 1 HETATM 2 C C2 NAG . . . U 4 215.187 219.296 274.654 1 121.07 ? C2 NAG 1002 D 1 HETATM 3 C C3 NAG . . . U 4 214.15 220.218 273.971 1 121.07 ? C3 NAG 1002 D 1 HETATM 4 C C4 NAG . . . U 4 213.164 220.784 274.986 1 121.07 ? C4 NAG 1002 D 1 HETATM 5 C C5 NAG . . . U 4 213.919 221.455 276.127 1 121.07 ? C5 NAG 1002 D 1 HETATM 6 C C6 NAG . . . U 4 213.006 222.01 277.195 1 121.07 ? C6 NAG 1002 D 1 HETATM 7 C C7 NAG . . . U 4 217.117 219.102 272.89 1 121.07 ? C7 NAG 1002 D 1 HETATM 8 C C8 NAG . . . U 4 217.496 220.576 272.889 1 121.07 ? C8 NAG 1002 D 1 HETATM 9 N N2 NAG . . . U 4 216.116 218.655 273.704 1 121.07 ? N2 NAG 1002 D 1 HETATM 10 O O3 NAG . . . U 4 213.456 219.489 272.966 1 121.07 ? O3 NAG 1002 D 1 HETATM 11 O O4 NAG . . . U 4 212.316 221.741 274.362 1 121.07 ? O4 NAG 1002 D 1 HETATM 12 O O5 NAG . . . U 4 214.763 220.487 276.768 1 121.07 ? O5 NAG 1002 D 1 HETATM 13 O O6 NAG . . . U 4 211.801 222.516 276.637 1 121.07 ? O6 NAG 1002 D 1 HETATM 14 O O7 NAG . . . U 4 217.721 218.312 272.174 1 121.07 ? O7 NAG 1002 D 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #