Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4426 |
| PDBID: | 7NBB |
| Chains: | D_A |
| Organism: | Homo sapiens, synthetic construct |
| Method: | XRD |
| Resolution (Å): | 1.55 |
| Reference: | Not available or To be published |
| Antibody | |
| Antibody: | NbSL3 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) |
| Antigen mutation: | Yes |
| Durg Target: | Q8ID50; P0CG47; P0CG47; P0CG47; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; P0CG48; |
Sequence information
Antibody
Chain: D
Mutation: NULL
| >7NBB_D|Chain D, H|Synthetic nanobody NbSL3|synthetic construct (32630) MGQVQLQESGGGLVQAGGSLRLSCAASGSIFDLGRMGWYRQAPGKEREFVAGIDYGGNTNYADSVKGRFTISRDNDTVYLQMNSLKPEDTAVYYCAAGIVGDVVGWIYYLYWGQGTQVTVSSGENLYFQ |
Antigen
Chain: A
Mutation: K48R/K63R
| >7NBB_A|Chain A, E|Polyubiquitin-B|Homo sapiens (9606) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR |
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)
| Chain residues position delta_SASA
: residuesposition D: LEU33 GLY34 ARG35 ASP54 TYR55 GLY56 ASN58 THR59 ASN60 ILE99 VAL100 GLY101 ASP102 VAL103 VAL104 GLY105 ILE107 A: MET1 PRO19 SER20 PHE45 ALA46 LYS48 LEU50 SER57 TYR59 ASN60 ILE61 GLN62 LYS63 SER65 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
