data_5GJV # _model_server_result.job_id c-0BYJjbPKCiLK83dWgZbA _model_server_result.datetime_utc '2025-04-02 18:40:38' _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 5gjv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"GA","auth_seq_id":1214}' # _entry.id 5GJV # _exptl.entry_id 5GJV _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 9 _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 5GJV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GJV _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,IA,JA,KA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 9 M N N ? 9 DA N N ? 9 EA N N ? 9 FA N N ? 9 GA N N ? 9 HA N N ? 9 IA N N ? 9 JA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 6 oligosaccharide 7 oligosaccharide 8 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 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 8 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 8 3 2 NAG NAG C1 O1 . O4 HO4 . 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 6 n F NAG 1 D 1 NAG F 1201 NAG 6 n F NAG 2 D 2 NAG F 1202 NAG 6 n G NAG 1 G 1 NAG F 1204 NAG 6 n G NAG 2 G 2 NAG F 1205 NAG 7 n H NAG 1 H 1 NAG F 1209 NAG 7 n H NAG 2 H 2 NAG F 1208 NAG 7 n H BMA 3 H 3 BMA F 1207 BMA 7 n I NAG 1 I 1 NAG F 1210 NAG 7 n I NAG 2 I 2 NAG F 1211 NAG 7 n I BMA 3 I 3 BMA F 1212 BMA 6 n J NAG 1 J 1 NAG F 1215 NAG 6 n J NAG 2 J 2 NAG F 1216 NAG 6 n K NAG 1 K 1 NAG F 1217 NAG 6 n K NAG 2 K 2 NAG F 1218 NAG 8 n L NAG 1 L 1 NAG F 1224 NAG 8 n L NAG 2 L 2 NAG F 1223 NAG 8 n L NAG 3 L 3 NAG F 1222 NAG # 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 226 A CYS 226 1_555 A SG CYS 254 A CYS 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf2 A SG CYS 245 A CYS 245 1_555 A SG CYS 261 A CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? disulf ? disulf3 A SG CYS 957 A CYS 957 1_555 A SG CYS 968 A CYS 968 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 1338 A CYS 1338 1_555 A SG CYS 1352 A CYS 1352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 D SG CYS 57 E CYS 57 1_555 D SG CYS 80 E CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 E SG CYS 305 F CYS 305 1_555 E SG CYS 1047 F CYS 1047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf7 E SG CYS 356 F CYS 356 1_555 E SG CYS 1062 F CYS 1062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? disulf ? disulf8 E SG CYS 406 F CYS 406 1_555 E SG CYS 1074 F CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.714 sing disulf ? disulf9 E SG CYS 907 F CYS 907 1_555 E SG CYS 977 F CYS 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 E SG CYS 999 F CYS 999 1_555 E SG CYS 1029 F CYS 1029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf11 E SG CYS 1002 F CYS 1002 1_555 E SG CYS 1027 F CYS 1027 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A ND2 ASN 257 A ASN 257 1_555 M C1 NAG . A NAG 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 E ND2 ASN 94 F ASN 94 1_555 FA C1 NAG . F NAG 1213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale3 E ND2 ASN 186 F ASN 186 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 E ND2 ASN 326 F ASN 326 1_555 DA C1 NAG . F NAG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale5 E ND2 ASN 350 F ASN 350 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 E ND2 ASN 470 F ASN 470 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 E ND2 ASN 606 F ASN 606 1_555 GA C1 NAG . F NAG 1214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale8 E ND2 ASN 615 F ASN 615 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale9 E ND2 ASN 678 F ASN 678 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 E ND2 ASN 784 F ASN 784 1_555 HA C1 NAG . F NAG 1219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 E ND2 ASN 827 F ASN 827 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale12 E ND2 ASN 891 F ASN 891 1_555 EA C1 NAG . F NAG 1206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 E ND2 ASN 898 F ASN 898 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale14 E ND2 ASN 988 F ASN 988 1_555 JA C1 NAG . F NAG 1221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale15 E ND2 ASN 1001 F ASN 1001 1_555 IA C1 NAG . F NAG 1220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale16 E C CYS 1074 F CYS 1074 1_555 E N ETA 1075 F ETA 1075 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? covale ? covale17 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale20 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale21 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale22 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale23 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale24 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale25 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale26 L O4 NAG . L NAG 2 1_555 L C1 NAG . L NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A OE2 GLU 292 A GLU 292 1_555 BA CA CA . A CA 1916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.023 ? metalc ? metalc2 A OE1 GLU 614 A GLU 614 1_555 BA CA CA . A CA 1916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.167 ? metalc ? metalc3 A OE1 GLU 1014 A GLU 1014 1_555 BA CA CA . A CA 1916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.167 ? metalc ? metalc4 E OG SER 265 F SER 265 1_555 KA CA CA . F CA 1225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? # _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 269 n n C1 O1 NAG sing 270 n n C1 O5 NAG sing 271 n n C1 H1 NAG sing 272 n n C2 C3 NAG sing 273 n n C2 N2 NAG sing 274 n n C2 H2 NAG sing 275 n n C3 C4 NAG sing 276 n n C3 O3 NAG sing 277 n n C3 H3 NAG sing 278 n n C4 C5 NAG sing 279 n n C4 O4 NAG sing 280 n n C4 H4 NAG sing 281 n n C5 C6 NAG sing 282 n n C5 O5 NAG sing 283 n n C5 H5 NAG sing 284 n n C6 O6 NAG sing 285 n n C6 H61 NAG sing 286 n n C6 H62 NAG sing 287 n n C7 C8 NAG sing 288 n n C7 N2 NAG sing 289 n n C7 O7 NAG doub 290 n n C8 H81 NAG sing 291 n n C8 H82 NAG sing 292 n n C8 H83 NAG sing 293 n n N2 HN2 NAG sing 294 n n O1 HO1 NAG sing 295 n n O3 HO3 NAG sing 296 n n O4 HO4 NAG sing 297 n n O6 HO6 NAG sing 298 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 5GJV _atom_sites.fract_transf_matrix[1][1] 0.002959 _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] 0.002959 _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] 0.002959 _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 M 9 NAG A 1 1901 1901 NAG NAG . N 10 PC1 A 1 1902 1902 PC1 PC1 . O 10 PC1 A 1 1903 1903 PC1 PC1 . P 10 PC1 A 1 1904 1904 PC1 PC1 . Q 10 PC1 A 1 1905 1905 PC1 PC1 . R 10 PC1 A 1 1906 1906 PC1 PC1 . S 10 PC1 A 1 1907 1907 PC1 PC1 . T 10 PC1 A 1 1908 1908 PC1 PC1 . U 10 PC1 A 1 1909 1909 PC1 PC1 . V 10 PC1 A 1 1910 1910 PC1 PC1 . W 10 PC1 A 1 1911 1911 PC1 PC1 . X 10 PC1 A 1 1912 1912 PC1 PC1 . Y 10 PC1 A 1 1913 1913 PC1 PC1 . Z 10 PC1 A 1 1914 1914 PC1 PC1 . AA 10 PC1 A 1 1915 1915 PC1 PC1 . BA 11 CA A 1 1916 1916 CA CA . CA 11 CA A 1 1917 1917 CA CA . DA 9 NAG F 1 1203 1203 NAG NAG . EA 9 NAG F 1 1206 1206 NAG NAG . FA 9 NAG F 1 1213 1213 NAG NAG . GA 9 NAG F 1 1214 1214 NAG NAG . HA 9 NAG F 1 1219 1219 NAG NAG . IA 9 NAG F 1 1220 1220 NAG NAG . JA 9 NAG F 1 1221 1221 NAG NAG . KA 11 CA F 1 1225 1225 CA CA . # 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 . . . GA 9 211.498 126.06 221.252 1 20 ? C1 NAG 1214 F 1 HETATM 2 C C2 NAG . . . GA 9 212.257 125.592 219.987 1 20 ? C2 NAG 1214 F 1 HETATM 3 C C3 NAG . . . GA 9 212.875 124.199 220.19 1 20 ? C3 NAG 1214 F 1 HETATM 4 C C4 NAG . . . GA 9 213.641 124.102 221.501 1 20 ? C4 NAG 1214 F 1 HETATM 5 C C5 NAG . . . GA 9 212.716 124.499 222.636 1 20 ? C5 NAG 1214 F 1 HETATM 6 C C6 NAG . . . GA 9 213.363 124.419 223.998 1 20 ? C6 NAG 1214 F 1 HETATM 7 C C7 NAG . . . GA 9 211.749 125.784 217.589 1 20 ? C7 NAG 1214 F 1 HETATM 8 C C8 NAG . . . GA 9 210.682 125.689 216.543 1 20 ? C8 NAG 1214 F 1 HETATM 9 N N2 NAG . . . GA 9 211.355 125.568 218.847 1 20 ? N2 NAG 1214 F 1 HETATM 10 O O3 NAG . . . GA 9 213.748 123.903 219.106 1 20 ? O3 NAG 1214 F 1 HETATM 11 O O4 NAG . . . GA 9 214.091 122.77 221.712 1 20 ? O4 NAG 1214 F 1 HETATM 12 O O5 NAG . . . GA 9 212.321 125.859 222.427 1 20 ? O5 NAG 1214 F 1 HETATM 13 O O6 NAG . . . GA 9 214.349 125.426 224.164 1 20 ? O6 NAG 1214 F 1 HETATM 14 O O7 NAG . . . GA 9 212.911 126.049 217.309 1 20 ? O7 NAG 1214 F 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #