data_7YG2 # _model_server_result.job_id aMq9rowlgjetUtXIGJDVxw _model_server_result.datetime_utc '2024-11-25 21:54:11' _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 7yg2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":601}' # _entry.id 7YG2 # _exptl.entry_id 7YG2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 _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 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 # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 M NAG 1 I 1 NAG J 160 NAG 4 n M NAG 2 I 2 NAG J 161 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 9 M CYS 162 1_555 A SG CYS 181 M CYS 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 15 M CYS 168 1_555 A SG CYS 170 M CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 205 M CYS 358 1_555 A SG CYS 293 M CYS 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 219 M CYS 372 1_555 A SG CYS 240 M CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 288 M CYS 441 1_555 A SG CYS 291 M CYS 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 174 A CYS 367 1_555 B SG CYS 233 A CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 281 A CYS 474 1_555 B SG CYS 343 A CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 C SG CYS 174 B CYS 367 1_555 C SG CYS 233 B CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 281 B CYS 474 1_555 C SG CYS 343 B CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 D SG CYS 174 C CYS 367 1_555 D SG CYS 233 C CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 D SG CYS 281 C CYS 474 1_555 D SG CYS 343 C CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 E SG CYS 174 D CYS 367 1_555 E SG CYS 233 D CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 E SG CYS 281 D CYS 474 1_555 E SG CYS 343 D CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 F SG CYS 281 E CYS 474 1_555 F SG CYS 343 E CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 G SG CYS 174 F CYS 367 1_555 G SG CYS 233 F CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf16 G SG CYS 281 F CYS 474 1_555 G SG CYS 343 F CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 H SG CYS 174 G CYS 367 1_555 H SG CYS 233 G CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf18 H SG CYS 281 G CYS 474 1_555 H SG CYS 343 G CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 I SG CYS 174 H CYS 367 1_555 I SG CYS 233 H CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf20 I SG CYS 281 H CYS 474 1_555 I SG CYS 343 H CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf21 J SG CYS 174 K CYS 367 1_555 J SG CYS 233 K CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf22 J SG CYS 281 K CYS 474 1_555 J SG CYS 343 K CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf23 K SG CYS 174 L CYS 367 1_555 K SG CYS 233 L CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf24 K SG CYS 281 L CYS 474 1_555 K SG CYS 343 L CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf25 K SG CYS 382 L CYS 575 1_555 L SG CYS 14 J CYS 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf26 L SG CYS 12 J CYS 12 1_555 L SG CYS 100 J CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf27 L SG CYS 108 J CYS 108 1_555 L SG CYS 133 J CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 B ND2 ASN 370 A ASN 563 1_555 N C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 C ND2 ASN 370 B ASN 563 1_555 O C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 D ND2 ASN 370 C ASN 563 1_555 P C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 E ND2 ASN 370 D ASN 563 1_555 Q C1 NAG . D NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 F ND2 ASN 370 E ASN 563 1_555 R C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 G ND2 ASN 370 F ASN 563 1_555 S C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 H ND2 ASN 370 G ASN 563 1_555 T C1 NAG . G NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 I ND2 ASN 370 H ASN 563 1_555 U C1 NAG . H NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale9 J ND2 ASN 370 K ASN 563 1_555 V C1 NAG . K NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale10 K ND2 ASN 370 L ASN 563 1_555 W C1 NAG . L NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 L ND2 ASN 48 J ASN 48 1_555 M C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale12 M O4 NAG . I NAG 1 1_555 M C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _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 7YG2 _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 N 5 NAG A 1 601 583 NAG NAG . O 5 NAG B 1 601 583 NAG NAG . P 5 NAG C 1 601 583 NAG NAG . Q 5 NAG D 1 601 583 NAG NAG . R 5 NAG E 1 601 583 NAG NAG . S 5 NAG F 1 601 583 NAG NAG . T 5 NAG G 1 601 583 NAG NAG . U 5 NAG H 1 601 583 NAG NAG . V 5 NAG K 1 601 583 NAG NAG . W 5 NAG L 1 601 583 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 . . . S 5 176.935 175.828 182.106 1 59.13 ? C1 NAG 601 F 1 HETATM 2 C C2 NAG . . . S 5 176.829 177.315 181.768 1 59.13 ? C2 NAG 601 F 1 HETATM 3 C C3 NAG . . . S 5 178.221 177.91 181.559 1 59.13 ? C3 NAG 601 F 1 HETATM 4 C C4 NAG . . . S 5 179.119 177.609 182.752 1 59.13 ? C4 NAG 601 F 1 HETATM 5 C C5 NAG . . . S 5 179.125 176.112 183.047 1 59.13 ? C5 NAG 601 F 1 HETATM 6 C C6 NAG . . . S 5 179.902 175.756 184.294 1 59.13 ? C6 NAG 601 F 1 HETATM 7 C C7 NAG . . . S 5 175.204 178.581 180.431 1 59.13 ? C7 NAG 601 F 1 HETATM 8 C C8 NAG . . . S 5 174.426 178.632 179.15 1 59.13 ? C8 NAG 601 F 1 HETATM 9 N N2 NAG . . . S 5 176.005 177.522 180.588 1 59.13 ? N2 NAG 601 F 1 HETATM 10 O O3 NAG . . . S 5 178.114 179.317 181.374 1 59.13 ? O3 NAG 601 F 1 HETATM 11 O O4 NAG . . . S 5 180.449 178.036 182.48 1 59.13 ? O4 NAG 601 F 1 HETATM 12 O O5 NAG . . . S 5 177.781 175.653 183.251 1 59.13 ? O5 NAG 601 F 1 HETATM 13 O O6 NAG . . . S 5 180.788 174.67 184.061 1 59.13 ? O6 NAG 601 F 1 HETATM 14 O O7 NAG . . . S 5 175.112 179.458 181.284 1 59.13 ? O7 NAG 601 F 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #