data_8YDR # _model_server_result.job_id FM4AIM4haiKRUYwRyKfqYQ _model_server_result.datetime_utc '2025-08-28 10:40:14' _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 8ydr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8YDR # _exptl.entry_id 8YDR _exptl.method 'X-RAY DIFFRACTION' # _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 1 _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 120 _cell.entry_id 8YDR _cell.length_a 73.69 _cell.length_b 73.69 _cell.length_c 99.82 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 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 _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 x,y,z _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B SG CYS 4 B CYS 336 1_555 B SG CYS 29 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 47 B CYS 379 1_555 B SG CYS 100 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 B SG CYS 59 B CYS 391 1_555 B SG CYS 193 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 B SG CYS 148 B CYS 480 1_555 B SG CYS 156 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 B ND2 ASN 11 B ASN 343 1_555 C C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 8YDR _atom_sites.fract_transf_matrix[1][1] 0.01357 _atom_sites.fract_transf_matrix[1][2] 0.007835 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01567 _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] 0.010018 _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 C 3 NAG B 1 601 601 NAG NAG . D 4 HOH A 1 101 20 HOH HOH . E 4 HOH B 1 701 3 HOH HOH . E 4 HOH B 2 702 40 HOH HOH . E 4 HOH B 3 703 10 HOH HOH . E 4 HOH B 4 704 19 HOH HOH . E 4 HOH B 5 705 5 HOH HOH . E 4 HOH B 6 706 1 HOH HOH . E 4 HOH B 7 707 7 HOH HOH . E 4 HOH B 8 708 23 HOH HOH . E 4 HOH B 9 709 38 HOH HOH . E 4 HOH B 10 710 16 HOH HOH . E 4 HOH B 11 711 9 HOH HOH . E 4 HOH B 12 712 6 HOH HOH . E 4 HOH B 13 713 22 HOH HOH . E 4 HOH B 14 714 8 HOH HOH . E 4 HOH B 15 715 14 HOH HOH . E 4 HOH B 16 716 12 HOH HOH . E 4 HOH B 17 717 13 HOH HOH . E 4 HOH B 18 718 2 HOH HOH . E 4 HOH B 19 719 11 HOH HOH . E 4 HOH B 20 720 24 HOH HOH . E 4 HOH B 21 721 25 HOH HOH . E 4 HOH B 22 722 41 HOH HOH . E 4 HOH B 23 723 32 HOH HOH . E 4 HOH B 24 724 15 HOH HOH . E 4 HOH B 25 725 29 HOH HOH . E 4 HOH B 26 726 18 HOH HOH . E 4 HOH B 27 727 30 HOH HOH . E 4 HOH B 28 728 39 HOH HOH . E 4 HOH B 29 729 28 HOH HOH . E 4 HOH B 30 730 4 HOH HOH . E 4 HOH B 31 731 36 HOH HOH . E 4 HOH B 32 732 26 HOH HOH . E 4 HOH B 33 733 37 HOH HOH . E 4 HOH B 34 734 34 HOH HOH . # 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 . . . C 3 19.651 54.596 19.141 1 69.5 ? C1 NAG 601 B 1 HETATM 2 C C2 NAG . . . C 3 19.795 54.2 17.668 1 67.19 ? C2 NAG 601 B 1 HETATM 3 C C3 NAG . . . C 3 21.225 54.447 17.19 1 69.08 ? C3 NAG 601 B 1 HETATM 4 C C4 NAG . . . C 3 21.626 55.893 17.448 1 71.96 ? C4 NAG 601 B 1 HETATM 5 C C5 NAG . . . C 3 21.453 56.221 18.927 1 71.76 ? C5 NAG 601 B 1 HETATM 6 C C6 NAG . . . C 3 21.725 57.673 19.246 1 74.72 ? C6 NAG 601 B 1 HETATM 7 C C7 NAG . . . C 3 18.592 52.417 16.483 1 61.26 ? C7 NAG 601 B 1 HETATM 8 C C8 NAG . . . C 3 18.32 50.944 16.409 1 55.39 ? C8 NAG 601 B 1 HETATM 9 N N2 NAG . . . C 3 19.421 52.811 17.456 1 62.26 ? N2 NAG 601 B 1 HETATM 10 O O3 NAG . . . C 3 21.315 54.15 15.801 1 69.12 ? O3 NAG 601 B 1 HETATM 11 O O4 NAG . . . C 3 22.982 56.107 17.069 1 72.91 ? O4 NAG 601 B 1 HETATM 12 O O5 NAG . . . C 3 20.098 55.96 19.328 1 74.46 ? O5 NAG 601 B 1 HETATM 13 O O6 NAG . . . C 3 20.603 58.492 18.949 1 70.15 ? O6 NAG 601 B 1 HETATM 14 O O7 NAG . . . C 3 18.082 53.212 15.701 1 64.43 ? O7 NAG 601 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #