data_7KF9 # _model_server_result.job_id 6HdEFqKqesUx1gOPuACSHQ _model_server_result.datetime_utc '2024-11-22 05:45:19' _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 7kf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":403}' # _entry.id 7KF9 # _exptl.entry_id 7KF9 _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 9 _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,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 ? 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 # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type 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 . O4 HO4 . sing 2 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 5 5 3 MAN BMA C1 O1 . O6 HO6 . 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 M NAG 1 M 1 NAG D 1563 NAG 5 n M NAG 2 M 2 NAG D 1564 NAG 5 n M BMA 3 M 3 BMA D 1565 BMA 5 n M MAN 4 M 4 MAN D 1567 MAN 5 n M MAN 5 M 5 MAN D 1566 MAN 5 n N NAG 1 N 1 NAG F 1563 NAG 5 n N NAG 2 N 2 NAG F 1564 NAG 5 n N BMA 3 N 3 BMA F 1565 BMA 5 n N MAN 4 N 4 MAN F 1567 MAN 5 n N MAN 5 N 5 MAN F 1566 MAN 5 n O NAG 1 O 1 NAG E 1563 NAG 5 n O NAG 2 O 2 NAG E 1564 NAG 5 n O BMA 3 O 3 BMA E 1565 BMA 5 n O MAN 4 O 4 MAN E 1567 MAN 5 n O MAN 5 O 5 MAN E 1566 MAN # 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 B SG CYS 125 A CYS 121 1_555 B SG CYS 151 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 C SG CYS 51 D CYS 511 1_555 C SG CYS 96 D CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 D SG CYS 40 J CYS 22 1_555 D SG CYS 107 J CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 F SG CYS 125 C CYS 121 1_555 F SG CYS 151 C CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 G SG CYS 51 F CYS 511 1_555 G SG CYS 96 F CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 H SG CYS 40 L CYS 22 1_555 H SG CYS 107 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf7 J SG CYS 125 B CYS 121 1_555 J SG CYS 151 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 K SG CYS 51 E CYS 511 1_555 K SG CYS 96 E CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf9 L SG CYS 40 K CYS 22 1_555 L SG CYS 107 K CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 B ND2 ASN 232 A ASN 228 1_555 R C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.523 ? covale ? covale2 B ND2 ASN 261 A ASN 257 1_555 P C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.531 ? covale ? covale3 B ND2 ASN 272 A ASN 268 1_555 Q C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.528 ? covale ? covale4 C ND2 ASN 103 D ASN 563 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale5 F ND2 ASN 232 C ASN 228 1_555 U C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? covale ? covale6 F ND2 ASN 261 C ASN 257 1_555 S C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.531 ? covale ? covale7 F ND2 ASN 272 C ASN 268 1_555 T C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.529 ? covale ? covale8 G ND2 ASN 103 F ASN 563 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.509 ? covale ? covale9 J ND2 ASN 232 B ASN 228 1_555 X C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? covale ? covale10 J ND2 ASN 261 B ASN 257 1_555 V C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.531 ? covale ? covale11 J ND2 ASN 272 B ASN 268 1_555 W C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.529 ? covale ? covale12 K ND2 ASN 103 E ASN 563 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.509 ? covale ? covale13 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale14 M O4 NAG . M NAG 2 1_555 M C1 BMA . M BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? covale ? covale15 M O3 BMA . M BMA 3 1_555 M C1 MAN . M MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.524 ? covale ? covale16 M O6 BMA . M BMA 3 1_555 M C1 MAN . M MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale17 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale18 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.517 ? covale ? covale19 N O3 BMA . N BMA 3 1_555 N C1 MAN . N MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.522 ? covale ? covale20 N O6 BMA . N BMA 3 1_555 N C1 MAN . N MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? covale ? covale21 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale22 O O4 NAG . O NAG 2 1_555 O C1 BMA . O BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.517 ? covale ? covale23 O O3 BMA . O BMA 3 1_555 O C1 MAN . O MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.523 ? covale ? covale24 O O6 BMA . O BMA 3 1_555 O C1 MAN . O MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 7KF9 _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 1258 NAG NAG . Q 6 NAG A 1 402 1268 NAG NAG . R 6 NAG A 1 403 1228 NAG NAG . S 6 NAG C 1 401 1258 NAG NAG . T 6 NAG C 1 402 1268 NAG NAG . U 6 NAG C 1 403 1228 NAG NAG . V 6 NAG B 1 401 1258 NAG NAG . W 6 NAG B 1 402 1268 NAG NAG . X 6 NAG B 1 403 1228 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 . . . X 6 140.24 137.3 160.759 1 238.03 ? C1 NAG 403 B 1 HETATM 2 C C2 NAG . . . X 6 140.54 138.376 159.613 1 238.16 ? C2 NAG 403 B 1 HETATM 3 C C3 NAG . . . X 6 139.209 138.629 158.821 1 241.2 ? C3 NAG 403 B 1 HETATM 4 C C4 NAG . . . X 6 138.707 137.269 158.206 1 242.09 ? C4 NAG 403 B 1 HETATM 5 C C5 NAG . . . X 6 138.488 136.222 159.36 1 241.02 ? C5 NAG 403 B 1 HETATM 6 C C6 NAG . . . X 6 138.095 134.836 158.844 1 244.46 ? C6 NAG 403 B 1 HETATM 7 C C7 NAG . . . X 6 142.345 140.042 160.078 1 233.1 ? C7 NAG 403 B 1 HETATM 8 C C8 NAG . . . X 6 142.859 141.293 160.728 1 234.05 ? C8 NAG 403 B 1 HETATM 9 N N2 NAG . . . X 6 141.067 139.626 160.241 1 236.28 ? N2 NAG 403 B 1 HETATM 10 O O3 NAG . . . X 6 139.447 139.577 157.763 1 239 ? O3 NAG 403 B 1 HETATM 11 O O4 NAG . . . X 6 137.474 137.492 157.517 1 244.54 ? O4 NAG 403 B 1 HETATM 12 O O5 NAG . . . X 6 139.755 136.054 160.136 1 238.21 ? O5 NAG 403 B 1 HETATM 13 O O6 NAG . . . X 6 137.708 133.967 159.906 1 242.42 ? O6 NAG 403 B 1 HETATM 14 O O7 NAG . . . X 6 143.148 139.398 159.396 1 229.59 ? O7 NAG 403 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #