data_8HDK # _model_server_result.job_id qzPHPF1oJxPBBnGXc9GumQ _model_server_result.datetime_utc '2024-11-21 13:39:15' _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 8hdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":803}' # _entry.id 8HDK # _exptl.entry_id 8HDK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 12 _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 8HDK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HDK _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 5 M N N ? 5 N N N ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 T N N ? 5 U N N ? 5 V N N ? 5 W N N ? 5 X N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 MAN 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 3 n E NAG 1 E 1 NAG A 901 NAG 3 n E NAG 2 E 2 NAG A 902 NAG 3 n F NAG 1 G 1 NAG A 905 NAG 3 n F NAG 2 G 2 NAG A 906 NAG 4 n G NAG 1 N 1 NAG A 921 NAG 4 n G NAG 2 N 2 NAG A 922 NAG 4 n G MAN 3 N 3 MAN A 923 MAN 4 n H NAG 1 R 1 NAG B 902 NAG 4 n H NAG 2 R 2 NAG B 903 NAG 4 n H MAN 3 R 3 MAN B 904 MAN 3 n I NAG 1 V 1 NAG C 905 NAG 3 n I NAG 2 V 2 NAG C 906 NAG 3 n J NAG 1 X 1 NAG C 913 NAG 3 n J NAG 2 X 2 NAG C 914 NAG 4 n K NAG 1 c 1 NAG C 921 NAG 4 n K NAG 2 c 2 NAG C 922 NAG 4 n K MAN 3 c 3 MAN C 923 MAN 3 n L NAG 1 g 1 NAG D 902 NAG 3 n L NAG 2 g 2 NAG D 903 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 79 A CYS 79 1_555 A SG CYS 308 A CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 420 A CYS 420 1_555 A SG CYS 454 A CYS 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 B SG CYS 82 B CYS 82 1_555 B SG CYS 317 B CYS 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 B SG CYS 426 B CYS 426 1_555 B SG CYS 453 B CYS 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 433 B CYS 433 1_555 B SG CYS 454 B CYS 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 C SG CYS 79 C CYS 79 1_555 C SG CYS 308 C CYS 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 C SG CYS 420 C CYS 420 1_555 C SG CYS 454 C CYS 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 C SG CYS 436 C CYS 436 1_555 C SG CYS 455 C CYS 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 D SG CYS 82 D CYS 82 1_555 D SG CYS 317 D CYS 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 D SG CYS 426 D CYS 426 1_555 D SG CYS 453 D CYS 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 D SG CYS 433 D CYS 433 1_555 D SG CYS 454 D CYS 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 D SG CYS 743 D CYS 743 1_555 D SG CYS 798 D CYS 798 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 61 A ASN 61 1_555 F C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 203 A ASN 203 1_555 M C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 239 A ASN 239 1_555 N C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A ND2 ASN 276 A ASN 276 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 A ND2 ASN 350 A ASN 350 1_555 O C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 A ND2 ASN 368 A ASN 368 1_555 P C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 A ND2 ASN 471 A ASN 471 1_555 Q C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale8 A ND2 ASN 771 A ASN 771 1_555 G C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 B ND2 ASN 337 B ASN 337 1_555 R C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 B ND2 ASN 685 B ASN 685 1_555 H C1 NAG . R NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale11 C ND2 ASN 239 C ASN 239 1_555 S C1 NAG . C NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 C ND2 ASN 276 C ASN 276 1_555 J C1 NAG . X NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale13 C ND2 ASN 350 C ASN 350 1_555 T C1 NAG . C NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale14 C ND2 ASN 368 C ASN 368 1_555 U C1 NAG . C NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale15 C ND2 ASN 471 C ASN 471 1_555 V C1 NAG . C NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale16 D ND2 ASN 337 D ASN 337 1_555 X C1 NAG . D NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.558 ? covale ? covale17 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale18 F O4 NAG . G NAG 1 1_555 F C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 G O4 NAG . N NAG 1 1_555 G C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale20 G O4 NAG . N NAG 2 1_555 G C1 MAN . N MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale21 H O4 NAG . R NAG 1 1_555 H C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale22 H O4 NAG . R NAG 2 1_555 H C1 MAN . R MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale23 I O4 NAG . V NAG 1 1_555 I C1 NAG . V NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale24 J O4 NAG . X NAG 1 1_555 J C1 NAG . X NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale25 K O4 NAG . c NAG 1 1_555 K C1 NAG . c NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale26 K O4 NAG . c NAG 2 1_555 K C1 MAN . c MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale27 L O4 NAG . g NAG 1 1_555 L C1 NAG . g NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 8HDK _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 5 NAG A 1 801 907 NAG NAG . N 5 NAG A 1 802 908 NAG NAG . O 5 NAG A 1 803 909 NAG NAG . P 5 NAG A 1 804 910 NAG NAG . Q 5 NAG A 1 805 911 NAG NAG . R 5 NAG B 1 901 901 NAG NAG . S 5 NAG C 1 801 902 NAG NAG . T 5 NAG C 1 802 915 NAG NAG . U 5 NAG C 1 803 916 NAG NAG . V 5 NAG C 1 804 917 NAG NAG . W 5 NAG C 1 805 924 NAG NAG . X 5 NAG D 1 901 905 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 . . . U 5 189.959 134.13 94.16 1 271.26 0 C1 NAG 803 C 1 HETATM 2 C C2 NAG . . . U 5 188.597 133.471 93.892 1 271.26 0 C2 NAG 803 C 1 HETATM 3 C C3 NAG . . . U 5 188.739 131.95 93.78 1 271.26 0 C3 NAG 803 C 1 HETATM 4 C C4 NAG . . . U 5 189.355 131.356 95.041 1 271.26 0 C4 NAG 803 C 1 HETATM 5 C C5 NAG . . . U 5 190.402 132.301 95.616 1 271.26 0 C5 NAG 803 C 1 HETATM 6 C C6 NAG . . . U 5 191.593 131.581 96.201 1 271.26 0 C6 NAG 803 C 1 HETATM 7 C C7 NAG . . . U 5 186.305 133.72 94.727 1 271.26 0 C7 NAG 803 C 1 HETATM 8 C C8 NAG . . . U 5 185.443 134.112 95.889 1 271.26 0 C8 NAG 803 C 1 HETATM 9 N N2 NAG . . . U 5 187.625 133.819 94.916 1 271.26 0 N2 NAG 803 C 1 HETATM 10 O O3 NAG . . . U 5 189.545 131.633 92.651 1 271.26 0 O3 NAG 803 C 1 HETATM 11 O O4 NAG . . . U 5 188.343 131.132 96.016 1 271.26 0 O4 NAG 803 C 1 HETATM 12 O O5 NAG . . . U 5 190.899 133.14 94.567 1 271.26 0 O5 NAG 803 C 1 HETATM 13 O O6 NAG . . . U 5 192.747 132.41 96.212 1 271.26 0 O6 NAG 803 C 1 HETATM 14 O O7 NAG . . . U 5 185.828 133.335 93.665 1 271.26 0 O7 NAG 803 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #