data_5BKG # _model_server_result.job_id a3LRaH1Kpcm6zBA0yVX43g _model_server_result.datetime_utc '2024-12-30 17:02:48' _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 5bkg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":502}' # _entry.id 5BKG # _exptl.entry_id 5BKG _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 5BKG _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BKG _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 _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 ? 3 F N N ? 3 G N N ? 3 I N N ? 3 J N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N # 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 145 A CYS 145 1_555 A SG CYS 159 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 205 A CYS 205 1_555 A SG CYS 216 A CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 145 B CYS 145 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 B SG CYS 205 B CYS 205 1_555 B SG CYS 216 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 C SG CYS 205 C CYS 205 1_555 C SG CYS 216 C CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 D SG CYS 205 D CYS 205 1_555 D SG CYS 216 D CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf7 E SG CYS 181 E CYS 161 1_555 E SG CYS 195 E CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 E SG CYS 241 E CYS 221 1_555 E SG CYS 253 E CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 45 A ASN 45 1_555 F C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 76 A ASN 76 1_555 G C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 B ND2 ASN 45 B ASN 45 1_555 I C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 76 B ASN 76 1_555 J C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 C ND2 ASN 45 C ASN 45 1_555 M C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 C ND2 ASN 76 C ASN 76 1_555 N C1 NAG . C NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 D ND2 ASN 45 D ASN 45 1_555 O C1 NAG . D NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 D ND2 ASN 76 D ASN 76 1_555 P C1 NAG . D NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 E ND2 ASN 240 E ASN 220 1_555 Q C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 5BKG _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 F 3 NAG A 1 501 501 NAG NAG . G 3 NAG A 1 502 502 NAG NAG . H 4 GLY A 1 503 601 GLY GLY . I 3 NAG B 1 501 501 NAG NAG . J 3 NAG B 1 502 502 NAG NAG . K 4 GLY B 1 503 601 GLY GLY . L 4 GLY B 1 504 601 GLY GLY . M 3 NAG C 1 501 501 NAG NAG . N 3 NAG C 1 502 502 NAG NAG . O 3 NAG D 1 501 501 NAG NAG . P 3 NAG D 1 502 502 NAG NAG . Q 3 NAG E 1 501 501 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 . . . P 3 128.944 84.722 152.451 1 41.09 ? C1 NAG 502 D 1 HETATM 2 C C2 NAG . . . P 3 129.956 84.277 151.382 1 41.09 ? C2 NAG 502 D 1 HETATM 3 C C3 NAG . . . P 3 130.259 82.785 151.514 1 41.09 ? C3 NAG 502 D 1 HETATM 4 C C4 NAG . . . P 3 130.663 82.44 152.939 1 41.09 ? C4 NAG 502 D 1 HETATM 5 C C5 NAG . . . P 3 129.587 82.917 153.904 1 41.09 ? C5 NAG 502 D 1 HETATM 6 C C6 NAG . . . P 3 129.939 82.679 155.353 1 41.09 ? C6 NAG 502 D 1 HETATM 7 C C7 NAG . . . P 3 129.152 85.804 149.629 1 41.09 ? C7 NAG 502 D 1 HETATM 8 C C8 NAG . . . P 3 128.66 85.913 148.218 1 41.09 ? C8 NAG 502 D 1 HETATM 9 N N2 NAG . . . P 3 129.465 84.573 150.045 1 41.09 ? N2 NAG 502 D 1 HETATM 10 O O3 NAG . . . P 3 131.307 82.436 150.616 1 41.09 ? O3 NAG 502 D 1 HETATM 11 O O4 NAG . . . P 3 130.829 81.033 153.074 1 41.09 ? O4 NAG 502 D 1 HETATM 12 O O5 NAG . . . P 3 129.406 84.33 153.748 1 41.09 ? O5 NAG 502 D 1 HETATM 13 O O6 NAG . . . P 3 128.785 82.369 156.121 1 41.09 ? O6 NAG 502 D 1 HETATM 14 O O7 NAG . . . P 3 129.257 86.783 150.359 1 41.09 ? O7 NAG 502 D 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #