data_6Y3Y # _model_server_result.job_id 7CV6Vkh2UJhE5XDwz7Vezg _model_server_result.datetime_utc '2025-08-03 09:28:48' _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 6y3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":407}' # _entry.id 6Y3Y # _exptl.entry_id 6Y3Y _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 6Y3Y _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y3Y _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 K N N ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O N N ? 6 P N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 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 ? 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 7 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 9 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 10 ? 5 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 C NAG 1 C 1 NAG A 1083 NAG 2 n C NAG 2 C 2 NAG A 1084 NAG 2 n C BMA 3 C 3 BMA A 1085 BMA 2 n C MAN 4 C 4 MAN A 1086 MAN 3 n D NAG 1 D 1 NAG A 1286 NAG 3 n D NAG 2 D 2 NAG A 1287 NAG 3 n D BMA 3 D 3 BMA A 1288 BMA 3 n D MAN 4 D 4 MAN A 1290 MAN 3 n D MAN 5 D 5 MAN A 1289 MAN 4 n E NAG 1 E 1 NAG A 1314 NAG 4 n E NAG 2 E 2 NAG A 1315 NAG 4 n E BMA 3 E 3 BMA A 1316 BMA 5 n F NAG 1 F 1 NAG A 1328 NAG 5 n F NAG 2 F 2 NAG A 1329 NAG 2 n G NAG 1 G 1 NAG B 1083 NAG 2 n G NAG 2 G 2 NAG B 1084 NAG 2 n G BMA 3 G 3 BMA B 1085 BMA 2 n G MAN 4 G 4 MAN B 1086 MAN 3 n H NAG 1 H 1 NAG B 1286 NAG 3 n H NAG 2 H 2 NAG B 1287 NAG 3 n H BMA 3 H 3 BMA B 1288 BMA 3 n H MAN 4 H 4 MAN B 1290 MAN 3 n H MAN 5 H 5 MAN B 1289 MAN 4 n I NAG 1 I 1 NAG B 1314 NAG 4 n I NAG 2 I 2 NAG B 1315 NAG 4 n I BMA 3 I 3 BMA B 1316 BMA 5 n J NAG 1 J 1 NAG B 1328 NAG 5 n J NAG 2 J 2 NAG B 1329 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 27 A CYS 38 1_555 A SG CYS 48 A CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 96 A CYS 107 1_555 A SG CYS 143 A CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 A SG CYS 169 A CYS 180 1_555 A SG CYS 235 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 177 A CYS 188 1_555 A SG CYS 208 A CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 266 A CYS 277 1_555 A SG CYS 271 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 A SG CYS 306 A CYS 317 1_555 A SG CYS 330 A CYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 B SG CYS 27 B CYS 38 1_555 B SG CYS 48 B CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 B SG CYS 96 B CYS 107 1_555 B SG CYS 143 B CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf9 B SG CYS 169 B CYS 180 1_555 B SG CYS 235 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 B SG CYS 177 B CYS 188 1_555 B SG CYS 208 B CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 266 B CYS 277 1_555 B SG CYS 271 B CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 B SG CYS 306 B CYS 317 1_555 B SG CYS 330 B CYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 72 A ASN 83 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 99 A ASN 110 1_555 K C1 NAG . A NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A ND2 ASN 134 A ASN 145 1_555 L C1 NAG . A NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 A ND2 ASN 182 A ASN 193 1_555 M C1 NAG . A NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 275 A ASN 286 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 A ND2 ASN 303 A ASN 314 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 A ND2 ASN 317 A ASN 328 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale8 B ND2 ASN 72 B ASN 83 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 B ND2 ASN 99 B ASN 110 1_555 N C1 NAG . B NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 B ND2 ASN 134 B ASN 145 1_555 O C1 NAG . B NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 B ND2 ASN 182 B ASN 193 1_555 P C1 NAG . B NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 B ND2 ASN 275 B ASN 286 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale13 B ND2 ASN 303 B ASN 314 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale14 B ND2 ASN 317 B ASN 328 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale15 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale16 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale17 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale18 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale20 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale21 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale22 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale23 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale24 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale25 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale26 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale27 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale28 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale29 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale30 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale31 H O6 BMA . H BMA 3 1_555 H C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale32 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale33 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale34 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _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 6Y3Y _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 K 6 NAG A 1 405 1110 NAG NAG . L 6 NAG A 1 406 1145 NAG NAG . M 6 NAG A 1 407 1193 NAG NAG . N 6 NAG B 1 405 1110 NAG NAG . O 6 NAG B 1 406 1145 NAG NAG . P 6 NAG B 1 407 1193 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 . . . M 6 122.401 143.249 162.075 0.44 76.65 ? C1 NAG 407 A 1 HETATM 2 C C2 NAG . . . M 6 121.687 143.669 163.36 0.44 76.65 ? C2 NAG 407 A 1 HETATM 3 C C3 NAG . . . M 6 121.338 145.155 163.305 0.44 76.65 ? C3 NAG 407 A 1 HETATM 4 C C4 NAG . . . M 6 122.579 145.99 163.013 0.44 76.65 ? C4 NAG 407 A 1 HETATM 5 C C5 NAG . . . M 6 123.281 145.483 161.753 0.44 76.65 ? C5 NAG 407 A 1 HETATM 6 C C6 NAG . . . M 6 124.6 146.173 161.494 0.44 76.65 ? C6 NAG 407 A 1 HETATM 7 C C7 NAG . . . M 6 120.45 141.846 164.44 0.44 76.65 ? C7 NAG 407 A 1 HETATM 8 C C8 NAG . . . M 6 119.137 141.133 164.547 0.44 76.65 ? C8 NAG 407 A 1 HETATM 9 N N2 NAG . . . M 6 120.493 142.87 163.582 0.44 76.65 ? N2 NAG 407 A 1 HETATM 10 O O3 NAG . . . M 6 120.764 145.553 164.545 0.44 76.65 ? O3 NAG 407 A 1 HETATM 11 O O4 NAG . . . M 6 122.217 147.354 162.828 0.44 76.65 ? O4 NAG 407 A 1 HETATM 12 O O5 NAG . . . M 6 123.568 144.08 161.875 0.44 76.65 ? O5 NAG 407 A 1 HETATM 13 O O6 NAG . . . M 6 125.69 145.399 161.975 0.44 76.65 ? O6 NAG 407 A 1 HETATM 14 O O7 NAG . . . M 6 121.429 141.508 165.097 0.44 76.65 ? O7 NAG 407 A 1 # _model_server_stats.io_time_ms 124 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #