data_5XW6 # _model_server_result.job_id yFGssTfN5CfUa6EBtYZjmQ _model_server_result.datetime_utc '2024-10-20 00:53:35' _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 5xw6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":402}' # _entry.id 5XW6 # _exptl.entry_id 5XW6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 5XW6 _cell.length_a 113.038 _cell.length_b 113.038 _cell.length_c 333.472 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XW6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 2 D N N ? 2 G N N ? 2 I 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 A SG CYS 86 C CYS 107 1_555 A SG CYS 135 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 A SG CYS 96 C CYS 117 1_555 A SG CYS 119 C CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf3 A SG CYS 102 C CYS 123 1_555 A SG CYS 129 C CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf4 A SG CYS 183 C CYS 204 1_555 A SG CYS 193 C CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 227 C CYS 248 1_555 A SG CYS 236 C CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 86 A CYS 107 1_555 B SG CYS 135 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf7 B SG CYS 96 A CYS 117 1_555 B SG CYS 119 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 B SG CYS 102 A CYS 123 1_555 B SG CYS 129 A CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf9 B SG CYS 183 A CYS 204 1_555 B SG CYS 193 A CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf10 B SG CYS 227 A CYS 248 1_555 B SG CYS 236 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf11 C SG CYS 86 B CYS 107 1_555 C SG CYS 135 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf12 C SG CYS 96 B CYS 117 1_555 C SG CYS 119 B CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf13 C SG CYS 102 B CYS 123 1_555 C SG CYS 129 B CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf14 C SG CYS 183 B CYS 204 1_555 C SG CYS 193 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf15 C SG CYS 227 B CYS 248 1_555 C SG CYS 236 B CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? covale ? covale1 A ND2 ASN 123 C ASN 144 1_555 D C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 B ND2 ASN 123 A ASN 144 1_555 G C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 C ND2 ASN 123 B ASN 144 1_555 I C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? # _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 302 n n C1 O1 NAG sing 303 n n C1 O5 NAG sing 304 n n C1 H1 NAG sing 305 n n C2 C3 NAG sing 306 n n C2 N2 NAG sing 307 n n C2 H2 NAG sing 308 n n C3 C4 NAG sing 309 n n C3 O3 NAG sing 310 n n C3 H3 NAG sing 311 n n C4 C5 NAG sing 312 n n C4 O4 NAG sing 313 n n C4 H4 NAG sing 314 n n C5 C6 NAG sing 315 n n C5 O5 NAG sing 316 n n C5 H5 NAG sing 317 n n C6 O6 NAG sing 318 n n C6 H61 NAG sing 319 n n C6 H62 NAG sing 320 n n C7 C8 NAG sing 321 n n C7 N2 NAG sing 322 n n C7 O7 NAG doub 323 n n C8 H81 NAG sing 324 n n C8 H82 NAG sing 325 n n C8 H83 NAG sing 326 n n N2 HN2 NAG sing 327 n n O1 HO1 NAG sing 328 n n O3 HO3 NAG sing 329 n n O4 HO4 NAG sing 330 n n O6 HO6 NAG sing 331 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 5XW6 _atom_sites.fract_transf_matrix[1][1] 0.008847 _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] 0.008847 _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] 0.002999 _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 D 2 NAG C 1 501 501 NAG NAG . E 3 128 C 1 502 401 128 128 . F 3 128 A 1 401 401 128 128 . G 2 NAG A 1 402 501 NAG NAG . H 3 128 B 1 401 401 128 128 . I 2 NAG B 1 402 501 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 . . . I 2 -30.497 -10.704 -49.245 1 69.42 ? C1 NAG 402 B 1 HETATM 2 C C2 NAG . . . I 2 -29.963 -11.505 -50.407 1 54.24 ? C2 NAG 402 B 1 HETATM 3 C C3 NAG . . . I 2 -30.769 -12.766 -50.248 1 61.91 ? C3 NAG 402 B 1 HETATM 4 C C4 NAG . . . I 2 -30.403 -13.435 -48.924 1 60.87 ? C4 NAG 402 B 1 HETATM 5 C C5 NAG . . . I 2 -30.351 -12.473 -47.73 1 55.26 ? C5 NAG 402 B 1 HETATM 6 C C6 NAG . . . I 2 -29.339 -12.946 -46.709 1 59.35 ? C6 NAG 402 B 1 HETATM 7 C C7 NAG . . . I 2 -29.417 -10.249 -52.448 1 80.09 ? C7 NAG 402 B 1 HETATM 8 C C8 NAG . . . I 2 -27.951 -10.47 -52.192 1 66.43 ? C8 NAG 402 B 1 HETATM 9 N N2 NAG . . . I 2 -30.296 -10.888 -51.67 1 73.78 ? N2 NAG 402 B 1 HETATM 10 O O3 NAG . . . I 2 -30.561 -13.609 -51.389 1 63.15 ? O3 NAG 402 B 1 HETATM 11 O O4 NAG . . . I 2 -31.406 -14.419 -48.661 1 72.77 ? O4 NAG 402 B 1 HETATM 12 O O5 NAG . . . I 2 -29.913 -11.162 -48.042 1 64.41 ? O5 NAG 402 B 1 HETATM 13 O O6 NAG . . . I 2 -30.115 -13.369 -45.596 1 75.43 ? O6 NAG 402 B 1 HETATM 14 O O7 NAG . . . I 2 -29.8 -9.517 -53.345 1 71.43 ? O7 NAG 402 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #