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The crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OME)-fmk
Analyse The crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DM9
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase isozyme L1; Tripeptide fluoromethyl ketone…
- EC
- 3.4.19.12, 6.-.-.-
- UniProt
- P09936
- Ligands
- PHQ, CF0
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12, 6.-.-.-) | protein | 223 | 39% helix, 19% strand | P09936 |
| X, Y | Tripeptide fluoromethyl ketone inhibitor Z-VAE(OME)-fmk | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 2 copies · chains A, X, B, Y
- CF0 · Fluoromethane · ion · 2 copies · chains A, X, B, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.47 | 0.76 | 28 | empty |
| 2 | 54 | 0.25 | 0.73 | 18 | empty |
| 3 | 51 | 0.24 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 588 Ų buried · 10 hydrogen bonds · protein-protein
- A–X · 328 Ų buried · 4 hydrogen bonds · protein-protein
- B–Y · 323 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4DM9 · The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a… · the same entry in another collection · chain A against A, TM-score 1.00
- P09936 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase isozyme L1… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P09936
- Elsewhere: RCSB PDB 4DM9 · PDBe 4DM9 · UniProt P09936
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