data_9JD9 # _model_server_result.job_id WV5pDuoTLRZ3tCCMEm4LSw _model_server_result.datetime_utc '2025-07-21 01:21:08' _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 9jd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":719}' # _entry.id 9JD9 # _exptl.entry_id 9JD9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 12 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 9JD9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JD9 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_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 _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 # _struct_asym.details ? _struct_asym.entity_id 12 _struct_asym.id T _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 162 A CYS 162 1_555 A SG CYS 171 A CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 190 A ASN 190 1_555 T C1 NAG . A NAG 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? metalc ? metalc1 A O GLY 56 A GLY 56 1_555 S NA NA . A NA 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc2 A O PHE 58 A PHE 58 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc3 A O VAL 59 A VAL 59 1_555 S NA NA . A NA 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc4 A O SER 301 A SER 301 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 A OG SER 301 A SER 301 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc6 A O LEU 398 A LEU 398 1_555 S NA NA . A NA 718 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.089 ? metalc ? metalc7 B O2 TAU . A TAU 701 1_555 R NA NA . A NA 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? # _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 417 n n C1 O1 NAG sing 418 n n C1 O5 NAG sing 419 n n C1 H1 NAG sing 420 n n C2 C3 NAG sing 421 n n C2 N2 NAG sing 422 n n C2 H2 NAG sing 423 n n C3 C4 NAG sing 424 n n C3 O3 NAG sing 425 n n C3 H3 NAG sing 426 n n C4 C5 NAG sing 427 n n C4 O4 NAG sing 428 n n C4 H4 NAG sing 429 n n C5 C6 NAG sing 430 n n C5 O5 NAG sing 431 n n C5 H5 NAG sing 432 n n C6 O6 NAG sing 433 n n C6 H61 NAG sing 434 n n C6 H62 NAG sing 435 n n C7 C8 NAG sing 436 n n C7 N2 NAG sing 437 n n C7 O7 NAG doub 438 n n C8 H81 NAG sing 439 n n C8 H82 NAG sing 440 n n C8 H83 NAG sing 441 n n N2 HN2 NAG sing 442 n n O1 HO1 NAG sing 443 n n O3 HO3 NAG sing 444 n n O4 HO4 NAG sing 445 n n O6 HO6 NAG sing 446 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 9JD9 _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 B 2 TAU A 1 701 601 TAU TAU . C 3 D12 A 1 702 602 D12 D12 . D 4 OCT A 1 703 603 OCT OCT . E 5 C14 A 1 704 604 C14 C14 . F 6 DD9 A 1 705 605 DD9 DD9 . G 7 HP6 A 1 706 606 HP6 HP6 . H 8 D10 A 1 707 607 D10 D10 . I 4 OCT A 1 708 608 OCT OCT . J 7 HP6 A 1 709 609 HP6 HP6 . K 3 D12 A 1 710 610 D12 D12 . L 4 OCT A 1 711 611 OCT OCT . M 4 OCT A 1 712 612 OCT OCT . N 8 D10 A 1 713 613 D10 D10 . O 3 D12 A 1 714 614 D12 D12 . P 9 HEX A 1 715 615 HEX HEX . Q 10 CL A 1 716 701 CL CL . R 11 NA A 1 717 702 NA NA . S 11 NA A 1 718 703 NA NA . T 12 NAG A 1 719 704 NAG NAG . U 13 HOH A 1 801 621 HOH HOH . U 13 HOH A 2 802 622 HOH HOH . # 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 12 161.133 127.541 111.876 1 30 ? C1 NAG 719 A 1 HETATM 2 C C2 NAG . . . T 12 161.998 128.678 111.327 1 30 ? C2 NAG 719 A 1 HETATM 3 C C3 NAG . . . T 12 163.389 128.166 110.941 1 30 ? C3 NAG 719 A 1 HETATM 4 C C4 NAG . . . T 12 164.006 127.337 112.065 1 30 ? C4 NAG 719 A 1 HETATM 5 C C5 NAG . . . T 12 163.007 126.277 112.503 1 30 ? C5 NAG 719 A 1 HETATM 6 C C6 NAG . . . T 12 163.573 125.398 113.604 1 30 ? C6 NAG 719 A 1 HETATM 7 C C7 NAG . . . T 12 160.574 130.371 110.26 1 30 ? C7 NAG 719 A 1 HETATM 8 C C8 NAG . . . T 12 159.877 130.787 108.996 1 30 ? C8 NAG 719 A 1 HETATM 9 N N2 NAG . . . T 12 161.37 129.299 110.174 1 30 ? N2 NAG 719 A 1 HETATM 10 O O3 NAG . . . T 12 164.216 129.285 110.599 1 30 ? O3 NAG 719 A 1 HETATM 11 O O4 NAG . . . T 12 165.147 126.597 111.615 1 30 ? O4 NAG 719 A 1 HETATM 12 O O5 NAG . . . T 12 161.808 126.899 112.947 1 30 ? O5 NAG 719 A 1 HETATM 13 O O6 NAG . . . T 12 163.751 126.213 114.753 1 30 ? O6 NAG 719 A 1 HETATM 14 O O7 NAG . . . T 12 160.415 130.987 111.306 1 30 ? O7 NAG 719 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #