data_8TOT # _model_server_result.job_id d2Zd3hgQaNzdKiGSN33zLA _model_server_result.datetime_utc '2025-01-13 17:18:41' _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 8tot # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":703}' # _entry.id 8TOT # _exptl.entry_id 8TOT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _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 116.93 _cell.angle_gamma 90 _cell.entry_id 8TOT _cell.length_a 111.661 _cell.length_b 89.308 _cell.length_c 118.508 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TOT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,J,K,L,M,T 1 1 B,D,H,I,N,O,P,Q,R,S 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 K N N ? 6 L N N ? 6 N N N ? 6 O N N ? 6 P N N ? 6 Q N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 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 3 n E NAG 1 E 1 NAG A 712 NAG 3 n E NAG 2 E 2 NAG A 713 NAG 3 n F NAG 1 F 1 NAG A 714 NAG 3 n F NAG 2 F 2 NAG A 715 NAG 3 n G NAG 1 G 1 NAG A 718 NAG 3 n G NAG 2 G 2 NAG A 719 NAG 3 n H NAG 1 H 1 NAG B 629 NAG 3 n H NAG 2 H 2 NAG B 630 NAG 4 n I NAG 1 I 1 NAG B 633 NAG 4 n I NAG 2 I 2 NAG B 634 NAG 4 n I BMA 3 I 3 BMA B 635 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 116 A CYS 133 1_555 A SG CYS 124 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 327 A CYS 344 1_555 A SG CYS 344 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 513 A CYS 530 1_555 A SG CYS 525 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 B SG CYS 116 B CYS 133 1_555 B SG CYS 124 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 B SG CYS 327 B CYS 344 1_555 B SG CYS 344 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 B SG CYS 513 B CYS 530 1_555 B SG CYS 525 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? covale ? covale1 A ND2 ASN 36 A ASN 53 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? covale ? covale2 A ND2 ASN 73 A ASN 90 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 A ND2 ASN 86 A ASN 103 1_555 K C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 A ND2 ASN 305 A ASN 322 1_555 L C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale5 A ND2 ASN 529 A ASN 546 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale6 B ND2 ASN 36 B ASN 53 1_555 N C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 B ND2 ASN 73 B ASN 90 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale8 B ND2 ASN 86 B ASN 103 1_555 O C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale9 B ND2 ASN 305 B ASN 322 1_555 P C1 NAG . B NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.567 ? covale ? covale10 B ND2 ASN 415 B ASN 432 1_555 Q C1 NAG . B NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale11 B ND2 ASN 529 B ASN 546 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale12 C C ACE 1 C ACE 0 1_555 C N TYR 2 C TYR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 C C CYS 14 C CYS 13 1_555 C N NH2 15 C NH2 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale14 D C ACE 1 D ACE 0 1_555 D N TYR 2 D TYR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale15 D C CYS 14 D CYS 13 1_555 D N NH2 15 D NH2 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale16 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale20 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale21 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? metalc ? metalc1 A NE2 HIS 357 A HIS 374 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc2 A NE2 HIS 361 A HIS 378 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc3 A OE1 GLU 385 A GLU 402 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc4 A OE2 GLU 385 A GLU 402 1_555 J ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 B NE2 HIS 357 B HIS 374 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc6 B OE2 GLU 358 B GLU 375 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc7 B NE2 HIS 361 B HIS 378 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc8 B OE2 GLU 385 B GLU 402 1_555 R ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? # _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 267 n n C1 O1 NAG sing 268 n n C1 O5 NAG sing 269 n n C1 H1 NAG sing 270 n n C2 C3 NAG sing 271 n n C2 N2 NAG sing 272 n n C2 H2 NAG sing 273 n n C3 C4 NAG sing 274 n n C3 O3 NAG sing 275 n n C3 H3 NAG sing 276 n n C4 C5 NAG sing 277 n n C4 O4 NAG sing 278 n n C4 H4 NAG sing 279 n n C5 C6 NAG sing 280 n n C5 O5 NAG sing 281 n n C5 H5 NAG sing 282 n n C6 O6 NAG sing 283 n n C6 H61 NAG sing 284 n n C6 H62 NAG sing 285 n n C7 C8 NAG sing 286 n n C7 N2 NAG sing 287 n n C7 O7 NAG doub 288 n n C8 H81 NAG sing 289 n n C8 H82 NAG sing 290 n n C8 H83 NAG sing 291 n n N2 HN2 NAG sing 292 n n O1 HO1 NAG sing 293 n n O3 HO3 NAG sing 294 n n O4 HO4 NAG sing 295 n n O6 HO6 NAG sing 296 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 8TOT _atom_sites.fract_transf_matrix[1][1] 0.008956 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004549 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011197 _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] 0.009465 _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 5 ZN A 1 701 701 ZN ZN . K 6 NAG A 1 702 716 NAG NAG . L 6 NAG A 1 703 717 NAG NAG . M 7 CL A 1 704 2 CL CL . N 6 NAG B 1 701 628 NAG NAG . O 6 NAG B 1 702 632 NAG NAG . P 6 NAG B 1 703 637 NAG NAG . Q 6 NAG B 1 704 638 NAG NAG . R 5 ZN B 1 705 7 ZN ZN . S 7 CL B 1 706 1 CL CL . T 8 HOH A 1 801 1 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 . . . P 6 38.076 17.413 -16.78 1 103.49 ? C1 NAG 703 B 1 HETATM 2 C C2 NAG . . . P 6 38.011 18.971 -16.711 1 104.22 ? C2 NAG 703 B 1 HETATM 3 C C3 NAG . . . P 6 38.045 19.462 -15.236 1 106.31 ? C3 NAG 703 B 1 HETATM 4 C C4 NAG . . . P 6 37.022 18.711 -14.384 1 107.33 ? C4 NAG 703 B 1 HETATM 5 C C5 NAG . . . P 6 37.27 17.211 -14.512 1 106.51 ? C5 NAG 703 B 1 HETATM 6 C C6 NAG . . . P 6 36.359 16.328 -13.688 1 107.53 ? C6 NAG 703 B 1 HETATM 7 C C7 NAG . . . P 6 39 19.95 -18.768 1 102.06 ? C7 NAG 703 B 1 HETATM 8 C C8 NAG . . . P 6 40.251 20.538 -19.37 1 101.52 ? C8 NAG 703 B 1 HETATM 9 N N2 NAG . . . P 6 39.093 19.573 -17.478 1 103.36 ? N2 NAG 703 B 1 HETATM 10 O O3 NAG . . . P 6 37.821 20.868 -15.157 1 107.12 ? O3 NAG 703 B 1 HETATM 11 O O4 NAG . . . P 6 37.077 19.106 -13.017 1 109.43 ? O4 NAG 703 B 1 HETATM 12 O O5 NAG . . . P 6 37.077 16.836 -15.879 1 104.67 ? O5 NAG 703 B 1 HETATM 13 O O6 NAG . . . P 6 36.374 14.984 -14.167 1 106.47 ? O6 NAG 703 B 1 HETATM 14 O O7 NAG . . . P 6 37.963 19.837 -19.424 1 101.48 ? O7 NAG 703 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #