Research workbench
The idol-UBE2D complex mediates sterol-dependent degradation of the LDL receptor
Analyse The idol-UBE2D complex mediates sterol-dependent degradation of the LDL receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YHN
- Type
- protein
- Length
- 128 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase mylip
- EC
- 6.3.2.-
- UniProt
- Q8WY64
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase mylip (EC 6.3.2.-) | protein | 64 | 20% helix, 22% strand | Q8WY64 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.58 | 0.85 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2YHN · The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WY64 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase mylip (Q8WY64) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q8WY64
- Elsewhere: RCSB PDB 2YHN · PDBe 2YHN · UniProt Q8WY64
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