data_6JP5 # _model_server_result.job_id 6aTf6UhZHjHYLLl_SdXitA _model_server_result.datetime_utc '2024-10-11 00:26:57' _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 6jp5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":1122}' # _entry.id 6JP5 # _exptl.entry_id 6JP5 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 9 _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 6JP5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JP5 _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details software_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 _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 ? 7 M N N ? 7 BA N N ? 7 CA N N ? 7 DA N N ? 7 EA N N ? 7 FA N N ? 7 GA N N ? 7 HA N N ? 7 IA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O3 HO3 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA 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 5 n F NAG 1 D 1 NAG F 1201 NAG 5 n F NAG 2 D 2 NAG F 1202 NAG 5 n G NAG 1 G 1 NAG F 1204 NAG 5 n G NAG 2 G 2 NAG F 1205 NAG 6 n H NAG 1 H 1 NAG F 1209 NAG 6 n H NAG 2 H 2 NAG F 1208 NAG 6 n H BMA 3 H 3 BMA F 1207 BMA 6 n I NAG 1 I 1 NAG F 1210 NAG 6 n I NAG 2 I 2 NAG F 1211 NAG 6 n I BMA 3 I 3 BMA F 1212 BMA 5 n J NAG 1 J 1 NAG F 1215 NAG 5 n J NAG 2 J 2 NAG F 1216 NAG 5 n K NAG 1 K 1 NAG F 1217 NAG 5 n K NAG 2 K 2 NAG F 1218 NAG 5 n L NAG 1 L 1 NAG F 1223 NAG 5 n L NAG 2 L 2 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? disulf ? disulf2 A SG CYS 957 A CYS 957 1_555 A SG CYS 968 A CYS 968 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf3 A SG CYS 1338 A CYS 1338 1_555 A SG CYS 1352 A CYS 1352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? disulf ? disulf4 B SG CYS 57 E CYS 57 1_555 B SG CYS 80 E CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 C SG CYS 305 F CYS 305 1_555 C SG CYS 1046 F CYS 1047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 C SG CYS 356 F CYS 356 1_555 C SG CYS 1061 F CYS 1062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? disulf ? disulf7 C SG CYS 406 F CYS 406 1_555 C SG CYS 1073 F CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? disulf ? disulf8 C SG CYS 669 F CYS 670 1_555 C SG CYS 699 F CYS 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf9 C SG CYS 906 F CYS 907 1_555 C SG CYS 976 F CYS 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 998 F CYS 999 1_555 C SG CYS 1028 F CYS 1029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf11 C SG CYS 1001 F CYS 1002 1_555 C SG CYS 1026 F CYS 1027 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? covale ? covale1 A ND2 ASN 257 A ASN 257 1_555 M C1 NAG . A NAG 1901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? covale ? covale2 C ND2 ASN 94 F ASN 92 1_555 DA C1 NAG . F NAG 1114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C ND2 ASN 186 F ASN 186 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 C ND2 ASN 470 F ASN 470 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.555 ? covale ? covale5 C ND2 ASN 606 F ASN 606 1_555 EA C1 NAG . F NAG 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale6 C ND2 ASN 615 F ASN 615 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.529 ? covale ? covale7 C ND2 ASN 826 F ASN 827 1_555 IA C1 NAG . F NAG 1125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale8 C ND2 ASN 890 F ASN 891 1_555 CA C1 NAG . F NAG 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale9 C ND2 ASN 897 F ASN 898 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale10 F O3 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale13 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale15 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 K O3 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale18 L O3 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A OD2 ASP 78 A ASP 78 1_555 Z CA CA . A CA 1914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc2 A OE1 GLU 292 A GLU 292 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.034 ? metalc ? metalc3 A OE2 GLU 292 A GLU 292 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc4 A OE1 GLU 292 A GLU 292 1_555 O CA CA . A CA 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc5 A OE1 GLU 1014 A GLU 1014 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc6 A OE2 GLU 1014 A GLU 1014 1_555 N CA CA . A CA 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc7 A OE2 GLU 1014 A GLU 1014 1_555 O CA CA . A CA 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? metalc ? metalc8 Z CA CA . A CA 1914 1_555 C OG SER 263 F SER 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc9 Z CA CA . A CA 1914 1_555 C OG SER 265 F SER 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc10 Z CA CA . A CA 1914 1_555 C OG1 THR 333 F THR 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _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 445 n n C1 O1 NAG sing 446 n n C1 O5 NAG sing 447 n n C1 H1 NAG sing 448 n n C2 C3 NAG sing 449 n n C2 N2 NAG sing 450 n n C2 H2 NAG sing 451 n n C3 C4 NAG sing 452 n n C3 O3 NAG sing 453 n n C3 H3 NAG sing 454 n n C4 C5 NAG sing 455 n n C4 O4 NAG sing 456 n n C4 H4 NAG sing 457 n n C5 C6 NAG sing 458 n n C5 O5 NAG sing 459 n n C5 H5 NAG sing 460 n n C6 O6 NAG sing 461 n n C6 H61 NAG sing 462 n n C6 H62 NAG sing 463 n n C7 C8 NAG sing 464 n n C7 N2 NAG sing 465 n n C7 O7 NAG doub 466 n n C8 H81 NAG sing 467 n n C8 H82 NAG sing 468 n n C8 H83 NAG sing 469 n n N2 HN2 NAG sing 470 n n O1 HO1 NAG sing 471 n n O3 HO3 NAG sing 472 n n O4 HO4 NAG sing 473 n n O6 HO6 NAG sing 474 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 6JP5 _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 M 7 NAG A 1 1901 1901 NAG NAG . N 8 CA A 1 1902 1902 CA CA . O 8 CA A 1 1903 1903 CA CA . P 9 3PE A 1 1904 10 3PE 3PE . Q 9 3PE A 1 1905 11 3PE 3PE . R 9 3PE A 1 1906 12 3PE 3PE . S 9 3PE A 1 1907 13 3PE 3PE . T 9 3PE A 1 1908 14 3PE 3PE . U 9 3PE A 1 1909 15 3PE 3PE . V 9 3PE A 1 1910 16 3PE 3PE . W 10 C5U A 1 1911 6 C5U LIG . X 11 PC1 A 1 1912 1 PC1 PC1 . Y 9 3PE A 1 1913 2 3PE 3PE . Z 8 CA A 1 1914 1904 CA CA . AA 12 ETA F 1 1101 1075 ETA ETA . BA 7 NAG F 1 1104 1203 NAG NAG . CA 7 NAG F 1 1107 1206 NAG NAG . DA 7 NAG F 1 1114 1213 NAG NAG . EA 7 NAG F 1 1115 1214 NAG NAG . FA 7 NAG F 1 1120 1219 NAG NAG . GA 7 NAG F 1 1121 1220 NAG NAG . HA 7 NAG F 1 1122 1221 NAG NAG . IA 7 NAG F 1 1125 1224 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 . . . HA 7 213.935 111.385 220.147 1 137.35 ? C1 NAG 1122 F 1 HETATM 2 C C2 NAG . . . HA 7 213.029 110.499 220.994 1 137.35 ? C2 NAG 1122 F 1 HETATM 3 C C3 NAG . . . HA 7 213.625 109.106 221.159 1 137.35 ? C3 NAG 1122 F 1 HETATM 4 C C4 NAG . . . HA 7 214.067 108.533 219.818 1 137.35 ? C4 NAG 1122 F 1 HETATM 5 C C5 NAG . . . HA 7 214.909 109.539 219.042 1 137.35 ? C5 NAG 1122 F 1 HETATM 6 C C6 NAG . . . HA 7 215.28 108.995 217.668 1 137.35 ? C6 NAG 1122 F 1 HETATM 7 C C7 NAG . . . HA 7 211.711 111.782 222.578 1 137.35 ? C7 NAG 1122 F 1 HETATM 8 C C8 NAG . . . HA 7 211.584 112.257 223.995 1 137.35 ? C8 NAG 1122 F 1 HETATM 9 N N2 NAG . . . HA 7 212.821 111.106 222.295 1 137.35 ? N2 NAG 1122 F 1 HETATM 10 O O3 NAG . . . HA 7 212.649 108.238 221.748 1 137.35 ? O3 NAG 1122 F 1 HETATM 11 O O4 NAG . . . HA 7 214.83 107.341 220.037 1 137.35 ? O4 NAG 1122 F 1 HETATM 12 O O5 NAG . . . HA 7 214.177 110.754 218.891 1 137.35 ? O5 NAG 1122 F 1 HETATM 13 O O6 NAG . . . HA 7 214.157 109.115 216.788 1 137.35 ? O6 NAG 1122 F 1 HETATM 14 O O7 NAG . . . HA 7 210.852 112.003 221.739 1 137.35 ? O7 NAG 1122 F 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #