data_7YG5 # _model_server_result.job_id y7gs0TmmfV-xTNx9Bb565Q _model_server_result.datetime_utc '2024-10-12 07:30:59' _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 7yg5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"FA","auth_seq_id":1207}' # _entry.id 7YG5 # _exptl.entry_id 7YG5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 11 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 8 _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 7YG5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YG5 _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA _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 ? 11 AA N N ? 11 BA N N ? 11 CA N N ? 11 DA N N ? 11 EA N N ? 11 FA N N ? 11 GA N N ? 11 HA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 5 3 2 BMA NAG C1 O1 . O3 HO3 . 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 4 n D NAG 1 E 1 NAG E 1235 NAG 4 n D NAG 2 E 2 NAG E 1236 NAG 4 n D BMA 3 E 3 BMA E 1237 BMA 4 n E NAG 1 C 1 NAG E 1241 NAG 4 n E NAG 2 C 2 NAG E 1242 NAG 4 n E BMA 3 C 3 BMA E 1243 BMA 5 n F NAG 1 F 1 NAG E 1247 NAG 5 n F NAG 2 F 2 NAG E 1248 NAG 5 n F BMA 3 F 3 BMA E 1249 BMA # 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 251 A CYS 251 1_555 A SG CYS 273 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 268 A CYS 268 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 1318 A CYS 1318 1_555 A SG CYS 1329 A CYS 1329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 A SG CYS 1678 A CYS 1678 1_555 A SG CYS 1694 A CYS 1694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 C SG CYS 303 D CYS 303 1_555 C SG CYS 1044 D CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 C SG CYS 354 D CYS 354 1_555 C SG CYS 1059 D CYS 1059 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf7 C SG CYS 404 D CYS 404 1_555 C SG CYS 1071 D CYS 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 C SG CYS 667 D CYS 667 1_555 C SG CYS 697 D CYS 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 904 D CYS 904 1_555 C SG CYS 974 D CYS 974 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf10 C SG CYS 996 D CYS 996 1_555 C SG CYS 1026 D CYS 1026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 C SG CYS 999 D CYS 999 1_555 C SG CYS 1024 D CYS 1024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 C ND2 ASN 92 D ASN 92 1_555 AA C1 NAG . D NAG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 C ND2 ASN 184 D ASN 184 1_555 HA C1 NAG . D NAG 1209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 324 D ASN 324 1_555 BA C1 NAG . D NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 C ND2 ASN 348 D ASN 348 1_555 CA C1 NAG . D NAG 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale5 C ND2 ASN 468 D ASN 468 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 C ND2 ASN 604 D ASN 604 1_555 DA C1 NAG . D NAG 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 C ND2 ASN 613 D ASN 613 1_555 EA C1 NAG . D NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale8 C ND2 ASN 675 D ASN 675 1_555 FA C1 NAG . D NAG 1207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 C ND2 ASN 824 D ASN 824 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 C ND2 ASN 888 D ASN 888 1_555 GA C1 NAG . D NAG 1208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 C ND2 ASN 895 D ASN 895 1_555 D C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale12 D O4 NAG . E NAG 1 1_555 D C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 D O4 NAG . E NAG 2 1_555 D C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale14 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale15 E O4 NAG . C NAG 2 1_555 E C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale17 F O3 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A OD2 ASP 116 A ASP 116 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc2 A OE1 GLU 309 A GLU 309 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc3 A OE2 GLU 309 A GLU 309 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc4 A OE1 GLU 1372 A GLU 1372 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc5 A O GLY 1662 A GLY 1662 1_555 U CA CA . A CA 2415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc6 C OG SER 261 D SER 261 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc7 C OG SER 263 D SER 263 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc8 C OG1 THR 331 D THR 331 1_555 Z CA CA . D CA 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? # _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 391 n n C1 O1 NAG sing 392 n n C1 O5 NAG sing 393 n n C1 H1 NAG sing 394 n n C2 C3 NAG sing 395 n n C2 N2 NAG sing 396 n n C2 H2 NAG sing 397 n n C3 C4 NAG sing 398 n n C3 O3 NAG sing 399 n n C3 H3 NAG sing 400 n n C4 C5 NAG sing 401 n n C4 O4 NAG sing 402 n n C4 H4 NAG sing 403 n n C5 C6 NAG sing 404 n n C5 O5 NAG sing 405 n n C5 H5 NAG sing 406 n n C6 O6 NAG sing 407 n n C6 H61 NAG sing 408 n n C6 H62 NAG sing 409 n n C7 C8 NAG sing 410 n n C7 N2 NAG sing 411 n n C7 O7 NAG doub 412 n n C8 H81 NAG sing 413 n n C8 H82 NAG sing 414 n n C8 H83 NAG sing 415 n n N2 HN2 NAG sing 416 n n O1 HO1 NAG sing 417 n n O3 HO3 NAG sing 418 n n O4 HO4 NAG sing 419 n n O6 HO6 NAG sing 420 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 7YG5 _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 6 Y01 A 1 2401 1902 Y01 Y01 . H 7 R16 A 1 2402 1903 R16 R16 . I 7 R16 A 1 2403 1904 R16 R16 . J 8 3PE A 1 2404 1905 3PE 3PE . K 8 3PE A 1 2405 1906 3PE 3PE . L 6 Y01 A 1 2406 1907 Y01 Y01 . M 7 R16 A 1 2407 1908 R16 R16 . N 6 Y01 A 1 2408 1909 Y01 Y01 . O 7 R16 A 1 2409 1910 R16 R16 . P 6 Y01 A 1 2410 1911 Y01 Y01 . Q 6 Y01 A 1 2411 1912 Y01 Y01 . R 6 Y01 A 1 2412 1913 Y01 Y01 . S 6 Y01 A 1 2413 1915 Y01 Y01 . T 6 Y01 A 1 2414 1916 Y01 Y01 . U 9 CA A 1 2415 1917 CA CA . V 10 TOR A 1 2416 1918 TOR TOR . W 6 Y01 A 1 2417 1919 Y01 Y01 . X 7 R16 A 1 2418 1925 R16 R16 . Y 7 R16 A 1 2419 1926 R16 R16 . Z 9 CA D 1 1201 1201 CA CA . AA 11 NAG D 1 1202 1238 NAG NAG . BA 11 NAG D 1 1203 1239 NAG NAG . CA 11 NAG D 1 1204 1240 NAG NAG . DA 11 NAG D 1 1205 1244 NAG NAG . EA 11 NAG D 1 1206 1245 NAG NAG . FA 11 NAG D 1 1207 1246 NAG NAG . GA 11 NAG D 1 1208 1250 NAG NAG . HA 11 NAG D 1 1209 1251 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 . . . FA 11 234.919 159.997 209.65 1 119.27 0 C1 NAG 1207 D 1 HETATM 2 C C2 NAG . . . FA 11 234.502 158.616 210.15 1 119.27 0 C2 NAG 1207 D 1 HETATM 3 C C3 NAG . . . FA 11 235.698 157.886 210.749 1 119.27 0 C3 NAG 1207 D 1 HETATM 4 C C4 NAG . . . FA 11 236.845 157.844 209.751 1 119.27 0 C4 NAG 1207 D 1 HETATM 5 C C5 NAG . . . FA 11 237.171 159.253 209.269 1 119.27 0 C5 NAG 1207 D 1 HETATM 6 C C6 NAG . . . FA 11 238.206 159.272 208.174 1 119.27 0 C6 NAG 1207 D 1 HETATM 7 C C7 NAG . . . FA 11 232.142 158.849 210.774 1 119.27 0 C7 NAG 1207 D 1 HETATM 8 C C8 NAG . . . FA 11 231.163 158.935 211.904 1 119.27 0 C8 NAG 1207 D 1 HETATM 9 N N2 NAG . . . FA 11 233.426 158.715 211.121 1 119.27 0 N2 NAG 1207 D 1 HETATM 10 O O3 NAG . . . FA 11 235.311 156.564 211.101 1 119.27 0 O3 NAG 1207 D 1 HETATM 11 O O4 NAG . . . FA 11 238 157.273 210.353 1 119.27 0 O4 NAG 1207 D 1 HETATM 12 O O5 NAG . . . FA 11 235.994 159.866 208.723 1 119.27 0 O5 NAG 1207 D 1 HETATM 13 O O6 NAG . . . FA 11 237.6 159.532 206.915 1 119.27 0 O6 NAG 1207 D 1 HETATM 14 O O7 NAG . . . FA 11 231.788 158.901 209.6 1 119.27 0 O7 NAG 1207 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 14 #