Research workbench
The catalytic domain of USP8 in complex with a USP8 specific inhibitor
Analyse The catalytic domain of USP8 in complex with a USP8 specific inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N3K
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 8; Ubiquitin
- EC
- 3.1.2.15
- UniProt
- P40818, P62988
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) | protein | 355 | 31% helix, 28% strand | P40818 |
| B | Ubiquitin | protein | 74 | 24% helix, 35% strand | P62988 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.80 | 0.84 | 60 | empty |
| 2 | 498 | 0.72 | 0.81 | 40 | empty |
| 3 | 169 | 0.49 | 0.77 | 27 | empty |
| 4 | 118 | 0.42 | 0.76 | 23 | empty |
| 5 | 110 | 0.39 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1485 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3N3K · The catalytic domain of USP8 in complex with a USP8 specific inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P40818 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 8 (P40818) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P40818
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 3N3K · PDBe 3N3K · UniProt P40818 · UniProt P62988
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