Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5136 |
| PDBID: | 7UBY |
| Chains: | C_A |
| Organism: | Clostridioides difficile, Camelidae |
| Method: | XRD |
| Resolution (Å): | 2.10 |
| Reference: | 10.3389/fimmu.2022.978858 |
| Antibody | |
| Antibody: | AH3 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Glucosyltransferase TcdA domain of Clostridium difficile toxin A |
| Antigen mutation: | Yes |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >7UBY_C|Chain B[auth C], D|Nanobody VHH AH3|Camelidae (9835) SQLQLVESGGGLVQPGGSLRLSCAASGFTLDYSSIGWFRQAPGKEREGVSCISSSGDSTKYADSVKGRFTTSRDNAKNTVYLQMNSLKPDDTAVYYCAAFRATMCGVFPLSPYGKDDWGKGTLVTVSSEPKTPKPQTSGAPVPYPDPLEPR |
Antigen
Chain: A
Mutation: K191A
| >7UBY_A|Chain A, C[auth B]|Glucosyltransferase TcdA|Clostridioides difficile (1496) SMSLISKEELIKLAYSIRPRENEYKTILTNLDEYNKLTTNNNENKYLQLKKLNESIDVFMNKYKTSSRNRALSNLKKDILKEVILIKNSNTSPVEKNLHFVWIGGEVSDIALEYIKQWADINAEYNIKLWYDSEAFLVNTLKKAIVESSTTEALQLLEEEIQNPQFDNMKFYKKRMEFIYDRQKRFINYYASQINKPTVPTIDDIIKSHLVSEYNRDETVLESYRTNSLRKINSNHGIDIRANSLFTEQELLNIYSQELLNRGNLAAASDIVRLLALKNFGGVYLDVDMLPGIHSDLFKTISRPSSIGLDRWEMIKLEAIMKYKKYINNYTSENFDKLDQQLKDNFKLIIESKSEKSEIFSKLENLNVSDLEIKIAFALGSVINQALISKQGSYLTNLVIEQVKNRYQFLNQHLNPAIESDNNFTDTTKIFHDSLFNSATAENSMFLTKIAPYLQVGFMPEARSTISLSGPGAYASAYYDFINLQENTIEKTLKASDLIEFKFPENNLSQLTEQEINSLWSFDQASAKYQFEKYVRDYTGGSL |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| C: GLN3 LEU4 PHE27 SER32 GLU44 ARG45 LYS59 ALA97 ALA98 PHE99 ARG100 ALA101 GLY105 VAL106 PHE107 PRO108 LEU109 SER110 PRO111 TYR112 GLY113 LYS114 ASP115 ASP116 A: GLU133 TYR189 ALA190 ILE193 ASN194 LYS195 PRO196 THR197 VAL198 PRO199 THR200 ASP203 ARG224 ARG240 ALA241 SER243 PHE245 THR246 GLU247 GLN248 GLU249 LEU251 ASN252 SER255 GLN256 LEU259 ASN260 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
