data_8Y8B # _model_server_result.job_id EP5Tyt94ZodXtcjMNt-JKQ _model_server_result.datetime_utc '2024-12-19 00:49:15' _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 8y8b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":1304}' # _entry.id 8Y8B # _exptl.entry_id 8Y8B _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 8Y8B _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y8B _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N,O,P,Q,R _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 ? 7 N N N ? 7 O N N ? 7 P N N ? 7 Q N N ? 7 R N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 5 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 3 n E NAG 1 D 1 NAG A 304 NAG 3 n E NAG 2 D 2 NAG A 305 NAG 3 n E BMA 3 D 3 BMA A 306 BMA 3 n E MAN 4 D 4 MAN A 307 MAN 4 n F NAG 1 E 1 NAG A 308 NAG 4 n F NAG 2 E 2 NAG A 322 NAG 4 n F BMA 3 E 3 BMA A 323 BMA 4 n G NAG 1 F 1 NAG A 312 NAG 4 n G NAG 2 F 2 NAG A 313 NAG 4 n G BMA 3 F 3 BMA A 314 BMA 5 n H NAG 1 G 1 NAG A 315 NAG 5 n H NAG 2 G 2 NAG A 316 NAG 5 n I NAG 1 H 1 NAG A 319 NAG 5 n I NAG 2 H 2 NAG A 320 NAG 5 n J NAG 1 I 1 NAG B 670 NAG 5 n J NAG 2 I 2 NAG B 671 NAG 5 n K NAG 1 J 1 NAG B 672 NAG 5 n K NAG 2 J 2 NAG B 673 NAG 5 n L NAG 1 K 1 NAG B 674 NAG 5 n L NAG 2 K 2 NAG B 675 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 7 A CYS 20 1_555 A SG CYS 143 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 138 A CYS 151 1_555 A SG CYS 170 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 150 A CYS 163 1_555 A SG CYS 229 A CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 314 B CYS 327 1_555 B SG CYS 339 B CYS 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 357 B CYS 370 1_555 B SG CYS 410 B CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 369 B CYS 382 1_555 B SG CYS 590 B CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 453 B CYS 466 1_555 B SG CYS 533 B CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 461 B CYS 474 1_555 B SG CYS 482 B CYS 495 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 463 B CYS 476 1_555 B SG CYS 552 B CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 472 B CYS 485 1_555 B SG CYS 503 B CYS 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 B SG CYS 491 B CYS 504 1_555 B SG CYS 505 B CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 B SG CYS 507 B CYS 520 1_555 B SG CYS 520 B CYS 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 B SG CYS 543 B CYS 556 1_555 B SG CYS 554 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 C SG CYS 77 C CYS 185 1_555 C SG CYS 133 C CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 C SG CYS 136 C CYS 244 1_555 D SG CYS 256 T CYS 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 D SG CYS 301 T CYS 410 1_555 D SG CYS 317 T CYS 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 D SG CYS 328 T CYS 437 1_555 D SG CYS 356 T CYS 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 6 A ASN 19 1_555 F C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale2 A ND2 ASN 16 A ASN 29 1_555 N C1 NAG . A NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 101 A ASN 114 1_555 P C1 NAG . A NAG 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 119 A ASN 132 1_555 E C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 A ND2 ASN 158 A ASN 171 1_555 O C1 NAG . A NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 175 A ASN 188 1_555 G C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale7 A ND2 ASN 179 A ASN 192 1_555 H C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 A ND2 ASN 238 A ASN 251 1_555 I C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 B ND2 ASN 322 B ASN 335 1_555 J C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 B ND2 ASN 342 B ASN 355 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 B ND2 ASN 420 B ASN 433 1_555 R C1 NAG . B NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 B ND2 ASN 441 B ASN 454 1_555 Q C1 NAG . B NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale13 B ND2 ASN 651 B ASN 664 1_555 K C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 E O4 NAG . D NAG 1 1_555 E C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale15 E O4 NAG . D NAG 2 1_555 E C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale16 E O3 BMA . D BMA 3 1_555 E C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale17 F O4 NAG . E NAG 1 1_555 F C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale18 F O4 NAG . E NAG 2 1_555 F C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 G O4 NAG . F NAG 1 1_555 G C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale20 G O4 NAG . F NAG 2 1_555 G C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale21 H O4 NAG . G NAG 1 1_555 H C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale22 I O4 NAG . H NAG 1 1_555 I C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale23 J O4 NAG . I NAG 1 1_555 J C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale24 K O4 NAG . J NAG 1 1_555 K C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale25 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 331 n n C1 O1 NAG sing 332 n n C1 O5 NAG sing 333 n n C1 H1 NAG sing 334 n n C2 C3 NAG sing 335 n n C2 N2 NAG sing 336 n n C2 H2 NAG sing 337 n n C3 C4 NAG sing 338 n n C3 O3 NAG sing 339 n n C3 H3 NAG sing 340 n n C4 C5 NAG sing 341 n n C4 O4 NAG sing 342 n n C4 H4 NAG sing 343 n n C5 C6 NAG sing 344 n n C5 O5 NAG sing 345 n n C5 H5 NAG sing 346 n n C6 O6 NAG sing 347 n n C6 H61 NAG sing 348 n n C6 H62 NAG sing 349 n n C7 C8 NAG sing 350 n n C7 N2 NAG sing 351 n n C7 O7 NAG doub 352 n n C8 H81 NAG sing 353 n n C8 H82 NAG sing 354 n n C8 H83 NAG sing 355 n n N2 HN2 NAG sing 356 n n O1 HO1 NAG sing 357 n n O3 HO3 NAG sing 358 n n O4 HO4 NAG sing 359 n n O6 HO6 NAG sing 360 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 8Y8B _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 M 6 MJJ A 1 1301 301 MJJ MJJ . N 7 NAG A 1 1302 317 NAG NAG . O 7 NAG A 1 1303 318 NAG NAG . P 7 NAG A 1 1304 321 NAG NAG . Q 7 NAG B 1 1301 676 NAG NAG . R 7 NAG B 1 1302 677 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 . . . P 7 108.67 119.55 141.554 1 98.64 ? C1 NAG 1304 A 1 HETATM 2 C C2 NAG . . . P 7 109.496 119.824 140.298 1 98.64 ? C2 NAG 1304 A 1 HETATM 3 C C3 NAG . . . P 7 108.641 119.624 139.05 1 98.64 ? C3 NAG 1304 A 1 HETATM 4 C C4 NAG . . . P 7 107.995 118.245 139.063 1 98.64 ? C4 NAG 1304 A 1 HETATM 5 C C5 NAG . . . P 7 107.232 118.031 140.367 1 98.64 ? C5 NAG 1304 A 1 HETATM 6 C C6 NAG . . . P 7 106.669 116.635 140.5 1 98.64 ? C6 NAG 1304 A 1 HETATM 7 C C7 NAG . . . P 7 111.371 121.407 140.294 1 98.64 ? C7 NAG 1304 A 1 HETATM 8 C C8 NAG . . . P 7 111.773 122.851 140.327 1 98.64 ? C8 NAG 1304 A 1 HETATM 9 N N2 NAG . . . P 7 110.057 121.165 140.324 1 98.64 ? N2 NAG 1304 A 1 HETATM 10 O O3 NAG . . . P 7 109.453 119.771 137.891 1 98.64 ? O3 NAG 1304 A 1 HETATM 11 O O4 NAG . . . P 7 107.096 118.119 137.967 1 98.64 ? O4 NAG 1304 A 1 HETATM 12 O O5 NAG . . . P 7 108.11 118.231 141.485 1 98.64 ? O5 NAG 1304 A 1 HETATM 13 O O6 NAG . . . P 7 107.702 115.669 140.639 1 98.64 ? O6 NAG 1304 A 1 HETATM 14 O O7 NAG . . . P 7 112.198 120.502 140.243 1 98.64 ? O7 NAG 1304 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 14 #