Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4431 |
| PDBID: | 7NBB |
| Chains: | H_G |
| 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: H
Mutation: NULL
| >7NBB_H|Chain D, H|Synthetic nanobody NbSL3|synthetic construct (32630) MGQVQLQESGGGLVQAGGSLRLSCAASGSIFDLGRMGWYRQAPGKEREFVAGIDYGGNTNYADSVKGRFTISRDNDTVYLQMNSLKPEDTAVYYCAAGIVGDVVGWIYYLYWGQGTQVTVSSGENLYFQ |
Antigen
Chain: G
Mutation: K48R/K63R
| >7NBB_G|Chain B, C, F, G|Polyubiquitin-B|Homo sapiens (9606) MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQRESTLHLVLRLRGG |
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 H: GLN5 TYR39 GLN41 GLU46 ARG47 PHE49 ASN60 ILE99 ASP102 VAL103 GLY105 TRP106 ILE107 TYR108 TYR109 LEU110 TYR111 TRP112 G: THR7 LEU8 THR9 GLU34 GLY35 ILE36 PRO37 ASP39 GLN40 ARG42 ILE44 GLN49 HIS68 LEU69 VAL70 LEU71 ARG72 LEU73 ARG74 GLY75 GLY76 |
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)
