data_3L89 # _model_server_result.job_id YIabN51Cjytn5mOLzUdn8g _model_server_result.datetime_utc '2024-10-19 10:28:44' _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 3l89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":1080}' # _entry.id 3L89 # _exptl.entry_id 3L89 _exptl.method 'X-RAY DIFFRACTION' # _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90.01 _cell.angle_beta 90.1 _cell.angle_gamma 104.7 _cell.entry_id 3L89 _cell.length_a 94.53 _cell.length_b 107.71 _cell.length_c 154.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3L89 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 PISA hexameric 6 author_and_software_defined_assembly 3 PISA hexameric 6 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,M,N,O,Y 1 1 D,E,F,P,Q,R,Z 2 1 G,H,I,S,T,U,AA 3 1 J,K,L,V,W,X,BA 4 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 ? 3 Y N N ? 3 Z N N ? 3 AA N N ? 3 BA 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 M SG CYS 1 M CYS 1 1_555 M SG CYS 46 M CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 M SG CYS 30 M CYS 30 1_555 M SG CYS 60 M CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 M SG CYS 65 M CYS 65 1_555 M SG CYS 107 M CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf4 M SG CYS 93 M CYS 93 1_555 M SG CYS 123 M CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 N SG CYS 1 N CYS 1 1_555 N SG CYS 46 N CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 N SG CYS 30 N CYS 30 1_555 N SG CYS 60 N CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 N SG CYS 65 N CYS 65 1_555 N SG CYS 107 N CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 N SG CYS 93 N CYS 93 1_555 N SG CYS 123 N CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 O SG CYS 1 O CYS 1 1_555 O SG CYS 46 O CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf10 O SG CYS 30 O CYS 30 1_555 O SG CYS 60 O CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf11 O SG CYS 65 O CYS 65 1_555 O SG CYS 107 O CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf12 O SG CYS 93 O CYS 93 1_555 O SG CYS 123 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf13 P SG CYS 1 P CYS 1 1_555 P SG CYS 46 P CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 P SG CYS 30 P CYS 30 1_555 P SG CYS 60 P CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 P SG CYS 65 P CYS 65 1_555 P SG CYS 107 P CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf16 P SG CYS 93 P CYS 93 1_555 P SG CYS 123 P CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 Q SG CYS 1 Q CYS 1 1_555 Q SG CYS 46 Q CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf18 Q SG CYS 30 Q CYS 30 1_555 Q SG CYS 60 Q CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf19 Q SG CYS 65 Q CYS 65 1_555 Q SG CYS 107 Q CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf20 Q SG CYS 93 Q CYS 93 1_555 Q SG CYS 123 Q CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf21 R SG CYS 1 R CYS 1 1_555 R SG CYS 46 R CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf22 R SG CYS 30 R CYS 30 1_555 R SG CYS 60 R CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf23 R SG CYS 65 R CYS 65 1_555 R SG CYS 107 R CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf24 R SG CYS 93 R CYS 93 1_555 R SG CYS 123 R CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf25 S SG CYS 1 S CYS 1 1_555 S SG CYS 46 S CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf26 S SG CYS 30 S CYS 30 1_555 S SG CYS 60 S CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf27 S SG CYS 65 S CYS 65 1_555 S SG CYS 107 S CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf28 S SG CYS 93 S CYS 93 1_555 S SG CYS 123 S CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf29 T SG CYS 1 T CYS 1 1_555 T SG CYS 46 T CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf30 T SG CYS 30 T CYS 30 1_555 T SG CYS 60 T CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf31 T SG CYS 65 T CYS 65 1_555 T SG CYS 107 T CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf32 T SG CYS 93 T CYS 93 1_555 T SG CYS 123 T CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf33 U SG CYS 1 U CYS 1 1_555 U SG CYS 46 U CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf34 U SG CYS 30 U CYS 30 1_555 U SG CYS 60 U CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf35 U SG CYS 65 U CYS 65 1_555 U SG CYS 107 U CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf36 U SG CYS 93 U CYS 93 1_555 U SG CYS 123 U CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf37 V SG CYS 1 V CYS 1 1_555 V SG CYS 46 V CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf38 V SG CYS 30 V CYS 30 1_555 V SG CYS 60 V CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf39 V SG CYS 65 V CYS 65 1_555 V SG CYS 107 V CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf40 V SG CYS 93 V CYS 93 1_555 V SG CYS 123 V CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf41 W SG CYS 1 W CYS 1 1_555 W SG CYS 46 W CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf42 W SG CYS 30 W CYS 30 1_555 W SG CYS 60 W CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf43 W SG CYS 65 W CYS 65 1_555 W SG CYS 107 W CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf44 W SG CYS 93 W CYS 93 1_555 W SG CYS 123 W CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf45 X SG CYS 1 X CYS 1 1_555 X SG CYS 46 X CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf46 X SG CYS 30 X CYS 30 1_555 X SG CYS 60 X CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf47 X SG CYS 65 X CYS 65 1_555 X SG CYS 107 X CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf48 X SG CYS 93 X CYS 93 1_555 X SG CYS 123 X CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 M ND2 ASN 80 M ASN 80 1_555 Y C1 NAG . M NAG 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 P ND2 ASN 80 P ASN 80 1_555 Z C1 NAG . P NAG 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 S ND2 ASN 80 S ASN 80 1_555 AA C1 NAG . S NAG 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale4 V ND2 ASN 80 V ASN 80 1_555 BA C1 NAG . V NAG 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? # _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 3L89 _atom_sites.fract_transf_matrix[1][1] 0.010579 _atom_sites.fract_transf_matrix[1][2] 0.002775 _atom_sites.fract_transf_matrix[1][3] 0.00002 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009598 _atom_sites.fract_transf_matrix[2][3] 0.000006 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006489 _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 Y 3 NAG M 1 1080 1080 NAG NAG . Z 3 NAG P 1 1080 1080 NAG NAG . AA 3 NAG S 1 1080 1080 NAG NAG . BA 3 NAG V 1 1080 1080 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 . . . AA 3 96.63 48.57 95.645 1 60.72 ? C1 NAG 1080 S 1 HETATM 2 C C2 NAG . . . AA 3 95.661 49.392 96.488 1 59.33 ? C2 NAG 1080 S 1 HETATM 3 C C3 NAG . . . AA 3 96.299 50.762 96.723 1 58.81 ? C3 NAG 1080 S 1 HETATM 4 C C4 NAG . . . AA 3 97.703 50.594 97.292 1 59.74 ? C4 NAG 1080 S 1 HETATM 5 C C5 NAG . . . AA 3 98.532 49.591 96.489 1 60.73 ? C5 NAG 1080 S 1 HETATM 6 C C6 NAG . . . AA 3 99.901 49.357 97.116 1 60.56 ? C6 NAG 1080 S 1 HETATM 7 C C7 NAG . . . AA 3 93.248 49.311 96.594 1 63.4 ? C7 NAG 1080 S 1 HETATM 8 C C8 NAG . . . AA 3 91.943 49.506 95.878 1 64.09 ? C8 NAG 1080 S 1 HETATM 9 N N2 NAG . . . AA 3 94.354 49.55 95.89 1 63.45 ? N2 NAG 1080 S 1 HETATM 10 O O3 NAG . . . AA 3 95.504 51.526 97.606 1 54.56 ? O3 NAG 1080 S 1 HETATM 11 O O4 NAG . . . AA 3 98.342 51.84 97.281 1 60.81 ? O4 NAG 1080 S 1 HETATM 12 O O5 NAG . . . AA 3 97.843 48.35 96.343 1 60.68 ? O5 NAG 1080 S 1 HETATM 13 O O6 NAG . . . AA 3 100.902 49.772 96.212 1 64.27 ? O6 NAG 1080 S 1 HETATM 14 O O7 NAG . . . AA 3 93.265 48.943 97.771 1 60.96 ? O7 NAG 1080 S 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #