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
- 3RIS
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- 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
- SO4
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 227 | 41% helix, 19% strand | Q9Y5K5 |
| B | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 227 | 40% helix, 19% strand | Q9Y5K5 |
| C | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 224 | 42% helix, 21% strand | Q9Y5K5 |
| D | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 222 | 40% helix, 21% strand | Q9Y5K5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.76 | 0.80 | 83 | empty |
| 2 | 218 | 0.55 | 0.78 | 28 | empty |
| 3 | 207 | 0.53 | 0.77 | 22 | empty |
| 4 | 102 | 0.50 | 0.81 | 19 | empty |
| 5 | 101 | 0.48 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 889 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 812 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 805 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3RIS · Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human… · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.91
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 3RIS · PDBe 3RIS · UniProt Q9Y5K5
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