data_8SK7 # _model_server_result.job_id QTJpSr---VETDr4p94FbOw _model_server_result.datetime_utc '2024-10-19 20:17:29' _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 8sk7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":401}' # _entry.id 8SK7 # _exptl.entry_id 8SK7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 _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 ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T N N ? 6 U N N ? 6 V N N ? 6 W N N ? 6 X N N ? 6 Y N N ? 6 Z N N ? 6 AA 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 # 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 J NAG 1 D 1 NAG A 1013 NAG 4 n J NAG 2 D 2 NAG A 1014 NAG 4 n J BMA 3 D 3 BMA A 1015 BMA 5 n K NAG 1 E 1 NAG A 1016 NAG 5 n K NAG 2 E 2 NAG A 1017 NAG 4 n L NAG 1 F 1 NAG B 1013 NAG 4 n L NAG 2 F 2 NAG B 1014 NAG 4 n L BMA 3 F 3 BMA B 1015 BMA 5 n M NAG 1 J 1 NAG B 1016 NAG 5 n M NAG 2 J 2 NAG B 1017 NAG 4 n N NAG 1 K 1 NAG C 1013 NAG 4 n N NAG 2 K 2 NAG C 1014 NAG 4 n N BMA 3 K 3 BMA C 1015 BMA 5 n O NAG 1 L 1 NAG C 1016 NAG 5 n O NAG 2 L 2 NAG C 1017 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 4 A CYS 14 1_555 B SG CYS 142 G CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 55 A CYS 65 1_555 A SG CYS 67 A CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 90 A CYS 100 1_555 A SG CYS 135 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 A SG CYS 278 A CYS 288 1_555 A SG CYS 302 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 B SG CYS 149 G CYS 144 1_555 B SG CYS 153 G CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 D SG CYS 4 B CYS 14 1_555 E SG CYS 142 H CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 D SG CYS 55 B CYS 65 1_555 D SG CYS 67 B CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 D SG CYS 90 B CYS 100 1_555 D SG CYS 135 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 D SG CYS 278 B CYS 288 1_555 D SG CYS 302 B CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf10 E SG CYS 149 H CYS 144 1_555 E SG CYS 153 H CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 G SG CYS 4 C CYS 14 1_555 H SG CYS 142 I CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 G SG CYS 55 C CYS 65 1_555 G SG CYS 67 C CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 G SG CYS 90 C CYS 100 1_555 G SG CYS 135 C CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf14 G SG CYS 278 C CYS 288 1_555 G SG CYS 302 C CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf15 H SG CYS 149 I CYS 144 1_555 H SG CYS 153 I CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 11 A ASN 21 1_555 Q C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 23 A ASN 33 1_555 K C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 87 A ASN 97 1_555 J C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A ND2 ASN 161 A ASN 171 1_555 P C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 A ND2 ASN 268 A ASN 278 1_555 R C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 286 A ASN 296 1_555 S C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 D ND2 ASN 11 B ASN 21 1_555 U C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 D ND2 ASN 23 B ASN 33 1_555 M C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 D ND2 ASN 87 B ASN 97 1_555 L C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale10 D ND2 ASN 161 B ASN 171 1_555 T C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D ND2 ASN 268 B ASN 278 1_555 V C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 D ND2 ASN 286 B ASN 296 1_555 W C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 G ND2 ASN 11 C ASN 21 1_555 Y C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 G ND2 ASN 23 C ASN 33 1_555 O C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale15 G ND2 ASN 87 C ASN 97 1_555 N C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale16 G ND2 ASN 161 C ASN 171 1_555 X C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale17 G ND2 ASN 268 C ASN 278 1_555 Z C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale18 G ND2 ASN 286 C ASN 296 1_555 AA C1 NAG . C NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 J O4 NAG . D NAG 1 1_555 J C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale20 J O4 NAG . D NAG 2 1_555 J C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale21 K O4 NAG . E NAG 1 1_555 K C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale22 L O4 NAG . F NAG 1 1_555 L C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale23 L O4 NAG . F NAG 2 1_555 L C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale24 M O4 NAG . J NAG 1 1_555 M C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale25 N O4 NAG . K NAG 1 1_555 N C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale26 N O4 NAG . K NAG 2 1_555 N C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale27 O O4 NAG . L NAG 1 1_555 O C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 8SK7 _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 P 6 NAG A 1 401 1009 NAG NAG . Q 6 NAG A 1 402 1010 NAG NAG . R 6 NAG A 1 403 1011 NAG NAG . S 6 NAG A 1 404 1012 NAG NAG . T 6 NAG B 1 401 1009 NAG NAG . U 6 NAG B 1 402 1010 NAG NAG . V 6 NAG B 1 403 1011 NAG NAG . W 6 NAG B 1 404 1012 NAG NAG . X 6 NAG C 1 401 1009 NAG NAG . Y 6 NAG C 1 402 1010 NAG NAG . Z 6 NAG C 1 403 1011 NAG NAG . AA 6 NAG C 1 404 1012 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 . . . T 6 133.293 164.148 200.582 1 50 ? C1 NAG 401 B 1 HETATM 2 C C2 NAG . . . T 6 133.134 165.299 199.598 1 50 ? C2 NAG 401 B 1 HETATM 3 C C3 NAG . . . T 6 131.808 166.011 199.843 1 50 ? C3 NAG 401 B 1 HETATM 4 C C4 NAG . . . T 6 130.657 165.011 199.817 1 50 ? C4 NAG 401 B 1 HETATM 5 C C5 NAG . . . T 6 130.938 163.843 200.76 1 50 ? C5 NAG 401 B 1 HETATM 6 C C6 NAG . . . T 6 129.901 162.747 200.67 1 50 ? C6 NAG 401 B 1 HETATM 7 C C7 NAG . . . T 6 134.798 166.833 198.65 1 50 ? C7 NAG 401 B 1 HETATM 8 C C8 NAG . . . T 6 135.936 167.765 198.946 1 50 ? C8 NAG 401 B 1 HETATM 9 N N2 NAG . . . T 6 134.243 166.232 199.708 1 50 ? N2 NAG 401 B 1 HETATM 10 O O3 NAG . . . T 6 131.615 167.005 198.844 1 50 ? O3 NAG 401 B 1 HETATM 11 O O4 NAG . . . T 6 129.451 165.651 200.217 1 50 ? O4 NAG 401 B 1 HETATM 12 O O5 NAG . . . T 6 132.202 163.243 200.438 1 50 ? O5 NAG 401 B 1 HETATM 13 O O6 NAG . . . T 6 130.289 161.602 201.416 1 50 ? O6 NAG 401 B 1 HETATM 14 O O7 NAG . . . T 6 134.399 166.636 197.506 1 50 ? O7 NAG 401 B 1 HETATM 15 H H1 NAG . . . T 6 133.309 164.495 201.495 1 50 ? H1 NAG 401 B 1 HETATM 16 H H2 NAG . . . T 6 133.115 164.932 198.694 1 50 ? H2 NAG 401 B 1 HETATM 17 H H3 NAG . . . T 6 131.835 166.44 200.72 1 50 ? H3 NAG 401 B 1 HETATM 18 H H4 NAG . . . T 6 130.551 164.667 198.909 1 50 ? H4 NAG 401 B 1 HETATM 19 H H5 NAG . . . T 6 130.97 164.174 201.678 1 50 ? H5 NAG 401 B 1 HETATM 20 H H61 NAG . . . T 6 129.052 163.083 201.017 1 50 ? H61 NAG 401 B 1 HETATM 21 H H62 NAG . . . T 6 129.785 162.494 199.734 1 50 ? H62 NAG 401 B 1 HETATM 22 H H81 NAG . . . T 6 135.591 168.58 199.359 1 50 ? H81 NAG 401 B 1 HETATM 23 H H82 NAG . . . T 6 136.558 167.331 199.56 1 50 ? H82 NAG 401 B 1 HETATM 24 H H83 NAG . . . T 6 136.397 167.989 198.115 1 50 ? H83 NAG 401 B 1 HETATM 25 H HN2 NAG . . . T 6 134.578 166.413 200.537 1 50 ? HN2 NAG 401 B 1 HETATM 26 H HO3 NAG . . . T 6 132.218 166.9 198.2 1 50 ? HO3 NAG 401 B 1 HETATM 27 H HO4 NAG . . . T 6 129.389 166.443 199.819 1 50 ? HO4 NAG 401 B 1 HETATM 28 H HO6 NAG . . . T 6 131.158 161.457 201.309 1 50 ? HO6 NAG 401 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #