Research workbench
System-wide modulation of hect E3 ligases with selective ubiquitin variant probes: NEDD4L and ubv NL.1
Analyse System-wide modulation of hect E3 ligases with selective ubiquitin variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HPK
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase NEDD4-like; Ubiquitin variant NL.1
- EC
- 6.3.2.-
- UniProt
- Q96PU5
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase NEDD4-like (EC 6.3.2.-) | protein | 372 | 50% helix, 14% strand | Q96PU5 |
| B | Ubiquitin variant NL.1 | protein | 78 | 23% helix, 35% strand | — |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.71 | 0.82 | 46 | empty |
| 2 | 553 | 0.65 | 0.76 | 65 | empty |
| 3 | 208 | 0.56 | 0.79 | 26 | empty |
| 4 | 142 | 0.48 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1118 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5HPK · System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96PU5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase NEDD4-like (Q96PU5) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 Q96PU5
- Elsewhere: RCSB PDB 5HPK · PDBe 5HPK · UniProt Q96PU5
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