Research workbench
Crystal structure of the catalytic domain of UCHL5, a proteasome- associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme
Analyse Crystal structure of the catalytic domain of UCHL5, a proteasome- associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RII
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase isozyme L5
- EC
- 3.4.19.12
- UniProt
- Q9Y5K5
- Ligands
- MG
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 212 | 36% helix, 20% strand | Q9Y5K5 |
| B | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 214 | 36% helix, 20% strand | Q9Y5K5 |
Ligands and binding sites
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 | 323 | 0.61 | 0.78 | 41 | EDO |
| 2 | 155 | 0.52 | 0.80 | 23 | empty |
| 3 | 110 | 0.49 | 0.81 | 21 | empty |
| 4 | 57 | 0.38 | 0.80 | 11 | empty |
| 5 | 60 | 0.38 | 0.80 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 300 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3RII · Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5K5 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase isozyme L5… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9Y5K5
- Elsewhere: RCSB PDB 3RII · PDBe 3RII · UniProt Q9Y5K5
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