Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6977 |
| PDBID: | 4NBY |
| Chains: | B_A |
| Organism: | Clostridioides difficile NAP07, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.08 |
| Reference: | 10.1074/jbc.M113.505917 |
| Antibody | |
| Antibody: | A20.1 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Rho-glucosylating toxins TcdA2 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >4NBY_B|Chain B, C|A20.1 VHH|Lama glama (9844) QPAMAQAQVQLVESGGGLAQAGGSLRLSCAASGRTFSMDPMAWFRQPPGKEREFVAAGSSTGRTTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAAPYGANWYRDEYAYWGQGTQVTVSSGQAGQGSEQKLISEEDLNHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >4NBY_A|Chain A|Cell wall-binding repeat protein|Clostridium difficile (525258) MHHHHHHSKAVTGMRTIDGKKYYFNTNTAEAATGWQTIDGKKYYFNTNTSIASTGYTIINDKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGRRYYFEPNTAIGANGYKIIDNKNFYFRNGLPQIGVFKGPNGFEYFAPANTDANNIDGQAIRYQNRFLHLLGNIYYFGNNSKAVTGWQTINGNMYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAPGIY |
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)
| B: GLN8 VAL9 GLY33 ARG34 THR35 SER37 MET38 ASP39 PRO40 SER59 SER60 THR61 THR64 TYR66 ALA106 PRO107 TYR108 GLY109 ALA110 ASN111 TRP112 ALA118 TYR119 A: ILE165 TYR176 PRO179 ALA180 ASN181 THR182 ASN185 TYR194 ARG197 PHE198 LEU199 HIS200 LEU201 LEU202 GLY203 ILE205 ASN222 ASN224 TYR226 VAL252 ASP253 |
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)
