data_6X9T # _model_server_result.job_id pAYOuiDgSJuyZ2AFkBoWmw _model_server_result.datetime_utc '2024-11-24 08:26:45' _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 6x9t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":603}' # _entry.id 6X9T # _exptl.entry_id 6X9T _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 17 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dodecameric 12 'complete point assembly' 1 ? tetrameric 4 'point asymmetric unit' 2 ? tetrameric 4 'point asymmetric unit, std point frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z 1 (1-3) A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z 3 P # 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] P 'transform to point frame' ? ? -0.705671 -0.70854 0.000387 0.70854 -0.70567 0.001224 -0.000594 0.001138 0.999999 232.96766 -0.62853 -141.67485 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? -0.499999 -0.866026 0.000094 0.866024 -0.499998 0.002222 -0.001877 0.001192 0.999998 389.83363 104.17631 0.11317 3 'point symmetry operation' ? ? -0.499999 0.866024 -0.001877 -0.866026 -0.499998 0.001192 0.000094 0.002222 0.999998 104.69767 389.69376 -0.3812 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 J N N ? 7 K N N ? 7 L N N ? 7 M N N ? 7 N N N ? 7 O N N ? 7 P N N ? 7 Q N N ? 7 R N N ? 7 S N N ? 7 T N N ? 7 U N N ? 7 V N N ? 7 W N N ? 7 X N N ? 7 Y N N ? 7 Z N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 MAN BMA C1 O1 . O3 HO3 . 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 5 n E NAG 1 C 1 NAG A 2327 NAG 5 n E NAG 2 C 2 NAG A 2328 NAG 5 n F NAG 1 D 1 NAG A 2330 NAG 5 n F NAG 2 D 2 NAG A 2331 NAG 6 n G NAG 1 E 1 NAG A 2333 NAG 6 n G NAG 2 E 2 NAG A 2334 NAG 6 n G BMA 3 E 3 BMA A 2335 BMA 6 n G MAN 4 E 4 MAN A 2336 MAN 5 n H NAG 1 F 1 NAG A 2344 NAG 5 n H NAG 2 F 2 NAG A 2345 NAG 5 n I NAG 1 G 1 NAG A 2347 NAG 5 n I NAG 2 G 2 NAG A 2348 NAG # 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 124 A CYS 119 1_555 A SG CYS 210 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 131 A CYS 126 1_555 A SG CYS 201 A CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 136 A CYS 131 1_555 A SG CYS 154 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 223 A CYS 218 1_555 A SG CYS 252 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 233 A CYS 228 1_555 A SG CYS 244 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? disulf ? disulf6 A SG CYS 301 A CYS 296 1_555 A SG CYS 335 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 382 A CYS 378 1_555 A SG CYS 448 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf8 A SG CYS 389 A CYS 385 1_555 A SG CYS 421 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf9 A SG CYS 504 A CYS 501 1_555 B SG CYS 94 B CYS 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? disulf ? disulf10 B SG CYS 87 B CYS 598 1_555 B SG CYS 93 B CYS 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf11 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf12 D SG CYS 20 L CYS 23 1_555 D SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 93 A ASN 88 1_555 J C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.393 ? covale ? covale2 A ND2 ASN 138 A ASN 133 1_555 K C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale3 A ND2 ASN 142 A ASN 137 1_555 L C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale4 A ND2 ASN 153 A ASN 156 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale5 A ND2 ASN 157 A ASN 160 1_555 M C1 NAG . A NAG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale6 A ND2 ASN 202 A ASN 197 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale7 A ND2 ASN 239 A ASN 234 1_555 N C1 NAG . A NAG 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale8 A ND2 ASN 267 A ASN 262 1_555 G C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale9 A ND2 ASN 281 A ASN 276 1_555 O C1 NAG . A NAG 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale10 A ND2 ASN 300 A ASN 295 1_555 P C1 NAG . A NAG 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale11 A ND2 ASN 306 A ASN 301 1_555 Q C1 NAG . A NAG 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale12 A ND2 ASN 336 A ASN 332 1_555 R C1 NAG . A NAG 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale13 A ND2 ASN 343 A ASN 339 1_555 S C1 NAG . A NAG 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale14 A ND2 ASN 359 A ASN 355 1_555 T C1 NAG . A NAG 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale15 A ND2 ASN 367 A ASN 363 1_555 U C1 NAG . A NAG 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale16 A ND2 ASN 390 A ASN 386 1_555 H C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale17 A ND2 ASN 396 A ASN 392 1_555 V C1 NAG . A NAG 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale18 A ND2 ASN 451 A ASN 448 1_555 I C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale19 B ND2 ASN 100 B ASN 611 1_555 W C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale20 B ND2 ASN 107 B ASN 618 1_555 X C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale21 B ND2 ASN 114 B ASN 625 1_555 Y C1 NAG . B NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale22 B ND2 ASN 126 B ASN 637 1_555 Z C1 NAG . B NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale23 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale24 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale25 G O4 NAG . E NAG 1 1_555 G C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale26 G O4 NAG . E NAG 2 1_555 G C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale27 G O3 BMA . E BMA 3 1_555 G C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale28 H O4 NAG . F NAG 1 1_555 H C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? covale ? covale29 I O4 NAG . G NAG 1 1_555 I C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 6X9T _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 J 7 NAG A 1 601 2324 NAG NAG . K 7 NAG A 1 602 2325 NAG NAG . L 7 NAG A 1 603 2326 NAG NAG . M 7 NAG A 1 606 2329 NAG NAG . N 7 NAG A 1 609 2332 NAG NAG . O 7 NAG A 1 614 2337 NAG NAG . P 7 NAG A 1 615 2338 NAG NAG . Q 7 NAG A 1 616 2339 NAG NAG . R 7 NAG A 1 617 2340 NAG NAG . S 7 NAG A 1 618 2341 NAG NAG . T 7 NAG A 1 619 2342 NAG NAG . U 7 NAG A 1 620 2343 NAG NAG . V 7 NAG A 1 623 2346 NAG NAG . W 7 NAG B 1 701 662 NAG NAG . X 7 NAG B 1 702 663 NAG NAG . Y 7 NAG B 1 703 664 NAG NAG . Z 7 NAG B 1 704 665 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 . . . L 7 125 154.723 202.027 1 59.21 ? C1 NAG 603 A 1 HETATM 2 C C2 NAG . . . L 7 125.829 155.698 202.821 1 61.49 ? C2 NAG 603 A 1 HETATM 3 C C3 NAG . . . L 7 124.948 156.628 203.557 1 68.4 ? C3 NAG 603 A 1 HETATM 4 C C4 NAG . . . L 7 124.04 157.392 202.535 1 66.88 ? C4 NAG 603 A 1 HETATM 5 C C5 NAG . . . L 7 123.188 156.345 201.765 1 74.58 ? C5 NAG 603 A 1 HETATM 6 C C6 NAG . . . L 7 122.26 156.981 200.771 1 73.55 ? C6 NAG 603 A 1 HETATM 7 C C7 NAG . . . L 7 127.83 155.232 204.099 1 49.04 ? C7 NAG 603 A 1 HETATM 8 C C8 NAG . . . L 7 128.473 154.359 205.123 1 55.3 ? C8 NAG 603 A 1 HETATM 9 N N2 NAG . . . L 7 126.591 154.958 203.809 1 66.2 ? N2 NAG 603 A 1 HETATM 10 O O3 NAG . . . L 7 125.755 157.544 204.34 1 62.67 ? O3 NAG 603 A 1 HETATM 11 O O4 NAG . . . L 7 123.211 158.277 203.213 1 77.81 ? O4 NAG 603 A 1 HETATM 12 O O5 NAG . . . L 7 124.067 155.478 201.055 1 63.3 ? O5 NAG 603 A 1 HETATM 13 O O6 NAG . . . L 7 121.389 157.911 201.399 1 70.7 ? O6 NAG 603 A 1 HETATM 14 O O7 NAG . . . L 7 128.417 156.17 203.548 1 55.77 ? O7 NAG 603 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #