data_1XWD # _model_server_result.job_id LCgljUhzdQXnjNNWP-hUnw _model_server_result.datetime_utc '2024-11-26 21:41:27' _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 1xwd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":112}' # _entry.id 1XWD # _exptl.entry_id 1XWD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.13 _cell.angle_gamma 90 _cell.entry_id 1XWD _cell.length_a 121.33 _cell.length_b 66.938 _cell.length_c 148.629 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XWD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,I,J,K,L,M,N,O,R,S,T 1 1 D,E,F,H,P,Q,U,V,W 2 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 ? 6 I N N ? 6 J N N ? 6 K N N ? 6 L N N ? 6 P N N ? 6 Q N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . 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 G NAG 1 G 1 NAG J 191 NAG 4 n G NAG 2 G 2 NAG J 192 NAG 5 n H NAG 1 H 1 NAG M 191 NAG 5 n H NAG 2 H 2 NAG M 192 NAG 5 n H BMA 3 H 3 BMA M 193 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 A SG CYS 7 A CYS 7 1_555 A SG CYS 31 A CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 10 A CYS 10 1_555 A SG CYS 60 A CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 A SG CYS 28 A CYS 28 1_555 A SG CYS 82 A CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 32 A CYS 32 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 A SG CYS 59 A CYS 59 1_555 A SG CYS 87 A CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 B SG CYS 3 B CYS 3 1_555 B SG CYS 51 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 B SG CYS 17 B CYS 17 1_555 B SG CYS 66 B CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 B SG CYS 20 B CYS 20 1_555 B SG CYS 104 B CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf9 B SG CYS 28 B CYS 28 1_555 B SG CYS 82 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf10 B SG CYS 32 B CYS 32 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 B SG CYS 87 B CYS 87 1_555 B SG CYS 94 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf12 C SG CYS 2 C CYS 18 1_555 C SG CYS 9 C CYS 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 C SG CYS 7 C CYS 23 1_555 C SG CYS 16 C CYS 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf14 D SG CYS 7 D CYS 7 1_555 D SG CYS 31 D CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 D SG CYS 10 D CYS 10 1_555 D SG CYS 60 D CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 D SG CYS 28 D CYS 28 1_555 D SG CYS 82 D CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf17 D SG CYS 32 D CYS 32 1_555 D SG CYS 84 D CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf18 D SG CYS 59 D CYS 59 1_555 D SG CYS 87 D CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf19 E SG CYS 3 E CYS 3 1_555 E SG CYS 51 E CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf20 E SG CYS 17 E CYS 17 1_555 E SG CYS 66 E CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf21 E SG CYS 20 E CYS 20 1_555 E SG CYS 104 E CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf22 E SG CYS 28 E CYS 28 1_555 E SG CYS 82 E CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf23 E SG CYS 32 E CYS 32 1_555 E SG CYS 84 E CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf24 E SG CYS 87 E CYS 87 1_555 E SG CYS 94 E CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf25 F SG CYS 2 F CYS 18 1_555 F SG CYS 9 F CYS 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf26 F SG CYS 7 F CYS 23 1_555 F SG CYS 16 F CYS 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 52 A ASN 52 1_555 I C1 NAG . A NAG 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 A ND2 ASN 78 A ASN 78 1_555 J C1 NAG . A NAG 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale3 B ND2 ASN 7 B ASN 7 1_555 K C1 NAG . B NAG 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B ND2 ASN 24 B ASN 24 1_555 L C1 NAG . B NAG 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale5 C ND2 ASN 175 C ASN 191 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 C ND2 ASN 175 C ASN 191 1_555 G C2 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? covale ? covale7 D ND2 ASN 78 D ASN 78 1_555 P C1 NAG . D NAG 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale8 E ND2 ASN 7 E ASN 7 1_555 Q C1 NAG . E NAG 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale9 F ND2 ASN 175 F ASN 191 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale10 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale11 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale12 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 1XWD _atom_sites.fract_transf_matrix[1][1] 0.008242 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001325 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014939 _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] 0.006814 _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 I 6 NAG A 1 93 52 NAG NAG . J 6 NAG A 1 94 78 NAG NAG . K 6 NAG B 1 112 7 NAG NAG . L 6 NAG B 1 113 24 NAG NAG . M 7 SO4 B 1 402 402 SO4 SO4 . N 7 SO4 B 1 403 403 SO4 SO4 . O 7 SO4 C 1 401 401 SO4 SO4 . P 6 NAG D 1 93 78 NAG NAG . Q 6 NAG E 1 112 7 NAG NAG . R 8 HOH A 1 95 1 HOH HOH . R 8 HOH A 2 96 10 HOH HOH . R 8 HOH A 3 97 11 HOH HOH . R 8 HOH A 4 98 47 HOH HOH . S 8 HOH B 1 404 9 HOH HOH . S 8 HOH B 2 405 19 HOH HOH . S 8 HOH B 3 406 24 HOH HOH . S 8 HOH B 4 407 28 HOH HOH . S 8 HOH B 5 408 30 HOH HOH . S 8 HOH B 6 409 37 HOH HOH . T 8 HOH C 1 402 2 HOH HOH . T 8 HOH C 2 403 3 HOH HOH . T 8 HOH C 3 404 6 HOH HOH . T 8 HOH C 4 405 7 HOH HOH . T 8 HOH C 5 406 13 HOH HOH . T 8 HOH C 6 407 15 HOH HOH . T 8 HOH C 7 408 18 HOH HOH . T 8 HOH C 8 409 23 HOH HOH . T 8 HOH C 9 410 36 HOH HOH . T 8 HOH C 10 411 42 HOH HOH . T 8 HOH C 11 412 45 HOH HOH . T 8 HOH C 12 413 48 HOH HOH . T 8 HOH C 13 414 49 HOH HOH . U 8 HOH D 1 94 14 HOH HOH . U 8 HOH D 2 95 41 HOH HOH . V 8 HOH E 1 113 17 HOH HOH . V 8 HOH E 2 114 34 HOH HOH . V 8 HOH E 3 115 43 HOH HOH . V 8 HOH E 4 116 44 HOH HOH . W 8 HOH F 1 272 4 HOH HOH . W 8 HOH F 2 273 5 HOH HOH . W 8 HOH F 3 274 8 HOH HOH . W 8 HOH F 4 275 12 HOH HOH . W 8 HOH F 5 276 16 HOH HOH . W 8 HOH F 6 277 20 HOH HOH . W 8 HOH F 7 278 21 HOH HOH . W 8 HOH F 8 279 22 HOH HOH . W 8 HOH F 9 280 25 HOH HOH . W 8 HOH F 10 281 26 HOH HOH . W 8 HOH F 11 282 27 HOH HOH . W 8 HOH F 12 283 29 HOH HOH . W 8 HOH F 13 284 31 HOH HOH . W 8 HOH F 14 285 32 HOH HOH . W 8 HOH F 15 286 33 HOH HOH . W 8 HOH F 16 287 35 HOH HOH . W 8 HOH F 17 288 38 HOH HOH . W 8 HOH F 18 289 39 HOH HOH . W 8 HOH F 19 290 40 HOH HOH . W 8 HOH F 20 291 46 HOH HOH . W 8 HOH F 21 292 50 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 . . . K 6 -9.187 10.749 46.975 1 76.97 ? C1 NAG 112 B 1 HETATM 2 C C2 NAG . . . K 6 -9.057 11.772 48.113 1 82.42 ? C2 NAG 112 B 1 HETATM 3 C C3 NAG . . . K 6 -10.437 12.136 48.692 1 83.39 ? C3 NAG 112 B 1 HETATM 4 C C4 NAG . . . K 6 -11.49 12.394 47.593 1 83.94 ? C4 NAG 112 B 1 HETATM 5 C C5 NAG . . . K 6 -11.504 11.326 46.486 1 83.46 ? C5 NAG 112 B 1 HETATM 6 C C6 NAG . . . K 6 -12.382 11.814 45.32 1 83.62 ? C6 NAG 112 B 1 HETATM 7 C C7 NAG . . . K 6 -7.315 11.92 49.902 1 84.63 ? C7 NAG 112 B 1 HETATM 8 C C8 NAG . . . K 6 -6.901 11.251 51.19 1 82.07 ? C8 NAG 112 B 1 HETATM 9 N N2 NAG . . . K 6 -8.17 11.217 49.137 1 83.31 ? N2 NAG 112 B 1 HETATM 10 O O3 NAG . . . K 6 -10.342 13.26 49.562 1 82.26 ? O3 NAG 112 B 1 HETATM 11 O O4 NAG . . . K 6 -12.788 12.521 48.148 1 84.02 ? O4 NAG 112 B 1 HETATM 12 O O5 NAG . . . K 6 -10.176 11.107 46.014 1 82 ? O5 NAG 112 B 1 HETATM 13 O O6 NAG . . . K 6 -12.557 10.828 44.317 1 84.55 ? O6 NAG 112 B 1 HETATM 14 O O7 NAG . . . K 6 -6.875 13.044 49.608 1 85.15 ? O7 NAG 112 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #