data_8YDT # _model_server_result.job_id u6OM4NbYne3ZfvBiRMERuw _model_server_result.datetime_utc '2025-08-28 08:06:20' _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 8ydt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 8YDT # _exptl.entry_id 8YDT _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 2 _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 8YDT _cell.length_a 73.307 _cell.length_b 73.307 _cell.length_c 99.799 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall 'P 31' _symmetry.space_group_name_H-M 'P 31' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E 1 1 C,D,F 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F 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 B SG CYS 4 B CYS 336 1_555 B SG CYS 29 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 47 B CYS 379 1_555 B SG CYS 100 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 59 B CYS 391 1_555 B SG CYS 193 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 B SG CYS 148 B CYS 480 1_555 B SG CYS 156 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 D SG CYS 4 D CYS 336 1_555 D SG CYS 29 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 D SG CYS 47 D CYS 379 1_555 D SG CYS 100 D CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 D SG CYS 59 D CYS 391 1_555 D SG CYS 193 D CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf8 D SG CYS 148 D CYS 480 1_555 D SG CYS 156 D CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 B ND2 ASN 11 B ASN 343 1_555 E C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale2 D ND2 ASN 11 D ASN 343 1_555 F C1 NAG . D NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _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 8YDT _atom_sites.fract_transf_matrix[1][1] 0.013641 _atom_sites.fract_transf_matrix[1][2] 0.007876 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015752 _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] 0.01002 _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 E 3 NAG B 1 601 601 NAG NAG . F 3 NAG D 1 601 601 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 . . . E 3 58.185 -12.384 45.463 1 112.37 ? C1 NAG 601 B 1 HETATM 2 C C2 NAG . . . E 3 57.927 -11.951 46.9 1 112.13 ? C2 NAG 601 B 1 HETATM 3 C C3 NAG . . . E 3 58.533 -10.569 47.15 1 115.66 ? C3 NAG 601 B 1 HETATM 4 C C4 NAG . . . E 3 60.018 -10.571 46.809 1 117.77 ? C4 NAG 601 B 1 HETATM 5 C C5 NAG . . . E 3 60.231 -11.059 45.377 1 117.9 ? C5 NAG 601 B 1 HETATM 6 C C6 NAG . . . E 3 61.691 -11.212 45.018 1 115.72 ? C6 NAG 601 B 1 HETATM 7 C C7 NAG . . . E 3 56.01 -12.238 48.398 1 110.03 ? C7 NAG 601 B 1 HETATM 8 C C8 NAG . . . E 3 54.522 -12.188 48.52 1 107.78 ? C8 NAG 601 B 1 HETATM 9 N N2 NAG . . . E 3 56.504 -11.951 47.191 1 105.97 ? N2 NAG 601 B 1 HETATM 10 O O3 NAG . . . E 3 58.348 -10.193 48.51 1 118.7 ? O3 NAG 601 B 1 HETATM 11 O O4 NAG . . . E 3 60.556 -9.259 46.949 1 115.84 ? O4 NAG 601 B 1 HETATM 12 O O5 NAG . . . E 3 59.62 -12.349 45.191 1 120.85 ? O5 NAG 601 B 1 HETATM 13 O O6 NAG . . . E 3 61.901 -12.331 44.168 1 111.07 ? O6 NAG 601 B 1 HETATM 14 O O7 NAG . . . E 3 56.734 -12.519 49.351 1 115.91 ? O7 NAG 601 B 1 # _model_server_stats.io_time_ms 135 _model_server_stats.parse_time_ms 162 _model_server_stats.create_model_time_ms 94 _model_server_stats.query_time_ms 499 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #