data_8DFY # _model_server_result.job_id GPPJfECFEIC_Y4m8lvaiIQ _model_server_result.datetime_utc '2024-11-22 21:45:29' _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 8dfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":302}' # _entry.id 8DFY # _exptl.entry_id 8DFY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.34 _cell.angle_gamma 90 _cell.entry_id 8DFY _cell.length_a 237.013 _cell.length_b 94.189 _cell.length_c 134.719 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DFY _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,F,H,I,N,O,P,T,U 1 1 B,G,Q,R,S 2 1,2 D,E,J,K,L,M,V,W,X,Y 3 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 N N N ? 4 O N N ? 4 P N N ? 4 Q N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 U N N ? 4 V N N ? 4 W N N ? 4 X N N ? 4 Y N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG 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 2 n F NAG 1 F 1 NAG A 220 NAG 2 n F NAG 2 F 2 NAG A 221 NAG 2 n F BMA 3 F 3 BMA A 222 BMA 2 n G NAG 1 G 1 NAG B 220 NAG 2 n G NAG 2 G 2 NAG B 221 NAG 2 n G BMA 3 G 3 BMA B 222 BMA 2 n H NAG 1 H 1 NAG C 220 NAG 2 n H NAG 2 H 2 NAG C 221 NAG 2 n H BMA 3 H 3 BMA C 222 BMA 2 n I NAG 1 I 1 NAG C 224 NAG 2 n I NAG 2 I 2 NAG C 225 NAG 2 n I BMA 3 I 3 BMA C 226 BMA 2 n J NAG 1 J 1 NAG D 220 NAG 2 n J NAG 2 J 2 NAG D 221 NAG 2 n J BMA 3 J 3 BMA D 222 BMA 3 n K NAG 1 K 1 NAG D 227 NAG 3 n K NAG 2 K 2 NAG D 228 NAG 2 n L NAG 1 L 1 NAG E 220 NAG 2 n L NAG 2 L 2 NAG E 221 NAG 2 n L BMA 3 L 3 BMA E 222 BMA 2 n M NAG 1 M 1 NAG E 224 NAG 2 n M NAG 2 M 2 NAG E 225 NAG 2 n M BMA 3 M 3 BMA E 226 BMA # 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 26 A CYS 23 1_555 A SG CYS 100 A CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 140 A CYS 137 1_555 A SG CYS 194 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf3 B SG CYS 26 B CYS 23 1_555 B SG CYS 100 B CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf4 B SG CYS 140 B CYS 137 1_555 B SG CYS 194 B CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf5 C SG CYS 26 C CYS 23 1_555 C SG CYS 100 C CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 C SG CYS 140 C CYS 137 1_555 C SG CYS 194 C CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? disulf ? disulf7 D SG CYS 26 D CYS 23 1_555 D SG CYS 100 D CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf8 D SG CYS 140 D CYS 137 1_555 D SG CYS 194 D CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf9 E SG CYS 26 E CYS 23 1_555 E SG CYS 100 E CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf10 E SG CYS 140 E CYS 137 1_555 E SG CYS 194 E CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 21 A ASN 18 1_555 P C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 89 A ASN 86 1_555 N C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 95 A ASN 92 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 A ND2 ASN 191 A ASN 188 1_555 O C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 B ND2 ASN 21 B ASN 18 1_555 S C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 89 B ASN 86 1_555 Q C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale7 B ND2 ASN 95 B ASN 92 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale8 B ND2 ASN 191 B ASN 188 1_555 R C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale9 C ND2 ASN 21 C ASN 18 1_555 U C1 NAG . C NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale10 C ND2 ASN 89 C ASN 86 1_555 T C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale11 C ND2 ASN 95 C ASN 92 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 C ND2 ASN 191 C ASN 188 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale13 D ND2 ASN 21 D ASN 18 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale14 D ND2 ASN 89 D ASN 86 1_555 V C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale15 D ND2 ASN 95 D ASN 92 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale16 D ND2 ASN 191 D ASN 188 1_555 W C1 NAG . D NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale17 E ND2 ASN 21 E ASN 18 1_555 Y C1 NAG . E NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale18 E ND2 ASN 89 E ASN 86 1_555 X C1 NAG . E NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale19 E ND2 ASN 95 E ASN 92 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale20 E ND2 ASN 191 E ASN 188 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale21 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale22 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale23 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale24 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale25 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale26 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale27 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale28 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale29 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale30 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale31 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale32 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale33 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale34 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale35 M O4 NAG . M NAG 2 1_555 M C1 BMA . M BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 8DFY _atom_sites.fract_transf_matrix[1][1] 0.004219 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001237 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010617 _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] 0.007735 _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 N 4 NAG A 1 301 223 NAG NAG . O 4 NAG A 1 302 224 NAG NAG . P 4 NAG A 1 303 227 NAG NAG . Q 4 NAG B 1 301 223 NAG NAG . R 4 NAG B 1 302 224 NAG NAG . S 4 NAG B 1 303 227 NAG NAG . T 4 NAG C 1 301 223 NAG NAG . U 4 NAG C 1 302 227 NAG NAG . V 4 NAG D 1 301 223 NAG NAG . W 4 NAG D 1 302 224 NAG NAG . X 4 NAG E 1 301 223 NAG NAG . Y 4 NAG E 1 302 227 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 . . . R 4 10.623 65.144 10.798 1 260.72 ? C1 NAG 302 B 1 HETATM 2 C C2 NAG . . . R 4 11.79 64.267 10.334 1 257.62 ? C2 NAG 302 B 1 HETATM 3 C C3 NAG . . . R 4 12.657 64.161 11.593 1 259.39 ? C3 NAG 302 B 1 HETATM 4 C C4 NAG . . . R 4 13.215 65.536 11.972 1 260.32 ? C4 NAG 302 B 1 HETATM 5 C C5 NAG . . . R 4 12.056 66.505 12.229 1 264.4 ? C5 NAG 302 B 1 HETATM 6 C C6 NAG . . . R 4 12.487 67.952 12.404 1 264.57 ? C6 NAG 302 B 1 HETATM 7 C C7 NAG . . . R 4 11.161 62.671 8.553 1 255.88 ? C7 NAG 302 B 1 HETATM 8 C C8 NAG . . . R 4 10.903 61.229 8.231 1 255.68 ? C8 NAG 302 B 1 HETATM 9 N N2 NAG . . . R 4 11.416 62.946 9.847 1 257.42 ? N2 NAG 302 B 1 HETATM 10 O O3 NAG . . . R 4 13.674 63.172 11.461 1 258.35 ? O3 NAG 302 B 1 HETATM 11 O O4 NAG . . . R 4 14.055 65.448 13.122 1 265.48 ? O4 NAG 302 B 1 HETATM 12 O O5 NAG . . . R 4 11.123 66.461 11.123 1 261.65 ? O5 NAG 302 B 1 HETATM 13 O O6 NAG . . . R 4 11.394 68.831 12.681 1 264.96 ? O6 NAG 302 B 1 HETATM 14 O O7 NAG . . . R 4 11.142 63.546 7.688 1 254.33 ? O7 NAG 302 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #