Research workbench
The ENTH domain from epsin-2 in complex with phosphatidylinositol 4,5-bisphosphate (PIP2)
Analyse The ENTH domain from epsin-2 in complex with phosphatidylinositol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ON7
- Type
- protein
- Length
- 289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.35
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- Epsin-2
- UniProt
- Q05785
- Ligands
- PIO, SO4
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · resolution 3.35 · 2 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epsin-2 | protein | 147 | 66% helix, 1% strand | Q05785 |
| B | Epsin-2 | protein | 142 | 68% helix, 1% strand | Q05785 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.61 | 0.78 | 35 | PIO |
| 2 | 75 | 0.39 | 0.78 | 18 | empty |
| 3 | 57 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 998 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5ON7 · The enth domain from epsin-2 in complex with phosphatidylinositol 4,5- bisphosphate (PIP2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q05785 · AlphaFold monomer V2.0 prediction for epsin-2 (Q05785) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q05785
- Elsewhere: RCSB PDB 5ON7 · PDBe 5ON7 · UniProt Q05785
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