data_8YDY # _model_server_result.job_id JoXRTnWTOLyibJiSILmvIQ _model_server_result.datetime_utc '2025-08-28 14:46:02' _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 8ydy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1301}' # _entry.id 8YDY # _exptl.entry_id 8YDY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _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 8YDY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YDY _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J 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 150 A CYS 131 1_555 A SG CYS 185 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 310 A CYS 291 1_555 A SG CYS 320 A CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 355 A CYS 336 1_555 A SG CYS 380 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 A SG CYS 398 A CYS 379 1_555 A SG CYS 451 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 A SG CYS 410 A CYS 391 1_555 A SG CYS 544 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 A SG CYS 499 A CYS 480 1_555 A SG CYS 507 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 A SG CYS 557 A CYS 538 1_555 A SG CYS 609 A CYS 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 A SG CYS 636 A CYS 617 1_555 A SG CYS 668 A CYS 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 A SG CYS 681 A CYS 662 1_555 A SG CYS 690 A CYS 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 A SG CYS 757 A CYS 738 1_555 A SG CYS 779 A CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 A SG CYS 762 A CYS 743 1_555 A SG CYS 768 A CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf12 A SG CYS 1051 A CYS 1032 1_555 A SG CYS 1062 A CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 A SG CYS 1101 A CYS 1082 1_555 A SG CYS 1145 A CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf14 B SG CYS 150 B CYS 131 1_555 B SG CYS 185 B CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 B SG CYS 310 B CYS 291 1_555 B SG CYS 320 B CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf16 B SG CYS 355 B CYS 336 1_555 B SG CYS 380 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf17 B SG CYS 398 B CYS 379 1_555 B SG CYS 451 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf18 B SG CYS 410 B CYS 391 1_555 B SG CYS 544 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf19 B SG CYS 499 B CYS 480 1_555 B SG CYS 507 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf20 B SG CYS 557 B CYS 538 1_555 B SG CYS 609 B CYS 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf21 B SG CYS 636 B CYS 617 1_555 B SG CYS 668 B CYS 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf22 B SG CYS 681 B CYS 662 1_555 B SG CYS 690 B CYS 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf23 B SG CYS 757 B CYS 738 1_555 B SG CYS 779 B CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf24 B SG CYS 762 B CYS 743 1_555 B SG CYS 768 B CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf25 B SG CYS 1051 B CYS 1032 1_555 B SG CYS 1062 B CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf26 B SG CYS 1101 B CYS 1082 1_555 B SG CYS 1145 B CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf27 C SG CYS 150 C CYS 131 1_555 C SG CYS 185 C CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf28 C SG CYS 310 C CYS 291 1_555 C SG CYS 320 C CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf29 C SG CYS 355 C CYS 336 1_555 C SG CYS 380 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf30 C SG CYS 398 C CYS 379 1_555 C SG CYS 451 C CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf31 C SG CYS 410 C CYS 391 1_555 C SG CYS 544 C CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf32 C SG CYS 499 C CYS 480 1_555 C SG CYS 507 C CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf33 C SG CYS 557 C CYS 538 1_555 C SG CYS 609 C CYS 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf34 C SG CYS 636 C CYS 617 1_555 C SG CYS 668 C CYS 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf35 C SG CYS 681 C CYS 662 1_555 C SG CYS 690 C CYS 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf36 C SG CYS 757 C CYS 738 1_555 C SG CYS 779 C CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf37 C SG CYS 762 C CYS 743 1_555 C SG CYS 768 C CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf38 C SG CYS 1051 C CYS 1032 1_555 C SG CYS 1062 C CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf39 C SG CYS 1101 C CYS 1082 1_555 C SG CYS 1145 C CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 B ND2 ASN 635 B ASN 616 1_555 G C1 NAG . B NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 B ND2 ASN 736 B ASN 717 1_555 H C1 NAG . B NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 B ND2 ASN 820 B ASN 801 1_555 I C1 NAG . B NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 C ND2 ASN 635 C ASN 616 1_555 J C1 NAG . C NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? # _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 8YDY _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 G 3 NAG B 1 1301 1303 NAG NAG . H 3 NAG B 1 1302 1305 NAG NAG . I 3 NAG B 1 1303 1306 NAG NAG . J 3 NAG C 1 1301 1303 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 . . . G 3 185.867 238.794 174.734 1 86.22 ? C1 NAG 1301 B 1 HETATM 2 C C2 NAG . . . G 3 184.797 239.212 175.739 1 86.22 ? C2 NAG 1301 B 1 HETATM 3 C C3 NAG . . . G 3 183.575 239.762 175.015 1 86.22 ? C3 NAG 1301 B 1 HETATM 4 C C4 NAG . . . G 3 183.976 240.857 174.037 1 86.22 ? C4 NAG 1301 B 1 HETATM 5 C C5 NAG . . . G 3 185.057 240.336 173.093 1 86.22 ? C5 NAG 1301 B 1 HETATM 6 C C6 NAG . . . G 3 185.556 241.406 172.142 1 86.22 ? C6 NAG 1301 B 1 HETATM 7 C C7 NAG . . . G 3 184.968 237.879 177.783 1 86.22 ? C7 NAG 1301 B 1 HETATM 8 C C8 NAG . . . G 3 184.48 236.663 178.508 1 86.22 ? C8 NAG 1301 B 1 HETATM 9 N N2 NAG . . . G 3 184.43 238.093 176.58 1 86.22 ? N2 NAG 1301 B 1 HETATM 10 O O3 NAG . . . G 3 182.643 240.251 175.97 1 86.22 ? O3 NAG 1301 B 1 HETATM 11 O O4 NAG . . . G 3 182.832 241.246 173.279 1 86.22 ? O4 NAG 1301 B 1 HETATM 12 O O5 NAG . . . G 3 186.183 239.874 173.865 1 86.22 ? O5 NAG 1301 B 1 HETATM 13 O O6 NAG . . . G 3 186.079 242.519 172.864 1 86.22 ? O6 NAG 1301 B 1 HETATM 14 O O7 NAG . . . G 3 185.825 238.619 178.257 1 86.22 ? O7 NAG 1301 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 71 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #