data_2YGQ # _model_server_result.job_id ZhXP2ZLWLGIBdEe160aY2g _model_server_result.datetime_utc '2025-02-16 23:00:37' _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 2ygq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1276}' # _entry.id 2YGQ # _exptl.entry_id 2YGQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _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 90 _cell.entry_id 2YGQ _cell.length_a 178.007 _cell.length_b 178.007 _cell.length_c 178.007 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 3 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GU4 _pdbx_entity_branch_link.comp_id_2 YYJ _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 B GU4 1 B 1 GU4 A 1279 SCR 2 n B YYJ 2 B 2 YYJ A 1279 SCR # 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 109 A CYS 140 1_555 A SG CYS 146 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 151 A CYS 182 1_555 A SG CYS 161 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 155 A CYS 186 1_555 A SG CYS 167 A CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 169 A CYS 200 1_555 A SG CYS 178 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 183 A CYS 214 1_555 A SG CYS 193 A CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 A SG CYS 187 A CYS 218 1_555 A SG CYS 199 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 A SG CYS 201 A CYS 232 1_555 A SG CYS 210 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 A SG CYS 215 A CYS 246 1_555 A SG CYS 225 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 A SG CYS 219 A CYS 250 1_555 A SG CYS 231 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 A SG CYS 233 A CYS 264 1_555 A SG CYS 242 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 57 A ASN 88 1_555 D C1 NAG . A NAG 1276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 214 A ASN 245 1_555 E C1 NAG . A NAG 1277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale3 A OG1 THR 224 A THR 255 1_555 F C1 FUC . A FUC 1278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 B C1 GU4 . B GU4 1 1_555 B O2 YYJ . B YYJ 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 sing # _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 298 n n C1 O1 NAG sing 299 n n C1 O5 NAG sing 300 n n C1 H1 NAG sing 301 n n C2 C3 NAG sing 302 n n C2 N2 NAG sing 303 n n C2 H2 NAG sing 304 n n C3 C4 NAG sing 305 n n C3 O3 NAG sing 306 n n C3 H3 NAG sing 307 n n C4 C5 NAG sing 308 n n C4 O4 NAG sing 309 n n C4 H4 NAG sing 310 n n C5 C6 NAG sing 311 n n C5 O5 NAG sing 312 n n C5 H5 NAG sing 313 n n C6 O6 NAG sing 314 n n C6 H61 NAG sing 315 n n C6 H62 NAG sing 316 n n C7 C8 NAG sing 317 n n C7 N2 NAG sing 318 n n C7 O7 NAG doub 319 n n C8 H81 NAG sing 320 n n C8 H82 NAG sing 321 n n C8 H83 NAG sing 322 n n N2 HN2 NAG sing 323 n n O1 HO1 NAG sing 324 n n O3 HO3 NAG sing 325 n n O4 HO4 NAG sing 326 n n O6 HO6 NAG sing 327 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 2YGQ _atom_sites.fract_transf_matrix[1][1] 0.005618 _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] 0.005618 _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] 0.005618 _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 PCF A 1 1275 1275 PCF PCF . D 4 NAG A 1 1276 1276 NAG NAG . E 4 NAG A 1 1277 1277 NAG NAG . F 5 FUC A 1 1278 1278 FUC FUC . # 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 . . . D 4 29.04 14.403 19.83 1 260.64 ? C1 NAG 1276 A 1 HETATM 2 C C2 NAG . . . D 4 28.024 13.646 20.687 1 263.6 ? C2 NAG 1276 A 1 HETATM 3 C C3 NAG . . . D 4 28.341 13.926 22.153 1 274.75 ? C3 NAG 1276 A 1 HETATM 4 C C4 NAG . . . D 4 29.765 13.437 22.411 1 264.54 ? C4 NAG 1276 A 1 HETATM 5 C C5 NAG . . . D 4 30.716 14.189 21.471 1 262.4 ? C5 NAG 1276 A 1 HETATM 6 C C6 NAG . . . D 4 32.146 13.697 21.722 1 255.46 ? C6 NAG 1276 A 1 HETATM 7 C C7 NAG . . . D 4 25.624 13.252 20.398 1 273.06 ? C7 NAG 1276 A 1 HETATM 8 C C8 NAG . . . D 4 24.238 13.755 20.087 1 276.73 ? C8 NAG 1276 A 1 HETATM 9 N N2 NAG . . . D 4 26.666 14.111 20.389 1 274.52 ? N2 NAG 1276 A 1 HETATM 10 O O3 NAG . . . D 4 27.427 13.236 23.007 1 279.39 ? O3 NAG 1276 A 1 HETATM 11 O O4 NAG . . . D 4 30.113 13.687 23.771 1 273.96 ? O4 NAG 1276 A 1 HETATM 12 O O5 NAG . . . D 4 30.373 13.944 20.099 1 253.23 ? O5 NAG 1276 A 1 HETATM 13 O O6 NAG . . . D 4 33.05 14.378 20.849 1 256.19 ? O6 NAG 1276 A 1 HETATM 14 O O7 NAG . . . D 4 25.795 12.079 20.662 1 263.61 ? O7 NAG 1276 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #