MolNFT v1 · #107582 · protein
Uch-L5 in complex with ubiquitin-propargyl bound to the RPN13 deubad domain
4UEL · Ubiquitin carboxyl-terminal hydrolase isozyme L5: “Uch-L5 in complex with ubiquitin-propargyl bound to the RPN13 deubad domain”. X-ray diffraction, 1 ligand (AYE), 5 pockets (best druggability 0.68). MolNFT v1 #107582 on GenesisL1…
- PDB
- 4UEL
- Type
- protein
- Length
- 475 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase isozyme L5; Polyubiquitin-B; Proteasomal ubiquitin…
- EC
- 3.4.19.12
- UniProt
- Q9Y5K5, P0CG47, Q16186
- Ligands
- AYE
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase isozyme L5 (EC 3.4.19.12) | protein | 302 | 48% helix, 16% strand | Q9Y5K5 |
| B | Polyubiquitin-B | protein | 75 | 24% helix, 35% strand | P0CG47 |
| C | Proteasomal ubiquitin receptor ADRM1 | protein | 98 | 70% helix, 2% strand | Q16186 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.68 | 0.80 | 40 | empty |
| 2 | 58 | 0.67 | 0.95 | 20 | empty |
| 3 | 272 | 0.52 | 0.75 | 36 | empty |
| 4 | 80 | 0.38 | 0.77 | 21 | empty |
| 5 | 89 | 0.33 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2253 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1177 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4UEL · UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain · 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 0.97
- Q16186 · AlphaFold monomer V2.0 prediction for proteasomal ubiquitin receptor ADRM1 (Q16186) · a predicted model of the same protein · chain C against A, TM-score 0.70
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
- Every structure of UniProt P0CG47
- Every structure of UniProt Q16186
- Elsewhere: RCSB PDB 4UEL · PDBe 4UEL · UniProt Q9Y5K5 · UniProt P0CG47 · UniProt Q16186
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