Research workbench
Crystal structure of the second StARkin domain of Lam2 in complex with ergosterol
Analyse Crystal structure of the second StARkin domain of Lam2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YS0
- Type
- protein
- Length
- 472 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.601
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- Membrane-anchored lipid-binding protein YSP2
- UniProt
- Q06681
- Ligands
- ERG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.601 · 3 distinct chains · 28% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-anchored lipid-binding protein YSP2 | protein | 160 | 26% helix, 41% strand | Q06681 |
| B | Membrane-anchored lipid-binding protein YSP2 | protein | 164 | 29% helix, 41% strand | Q06681 |
| C | Membrane-anchored lipid-binding protein YSP2 | protein | 148 | 27% helix, 36% strand | Q06681 |
Ligands and binding sites
- ERG · Ergosterol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.75 | 0.84 | 46 | ERG |
| 2 | 374 | 0.73 | 0.84 | 46 | ERG |
| 3 | 547 | 0.71 | 0.80 | 59 | empty |
| 4 | 242 | 0.54 | 0.77 | 24 | empty |
| 5 | 104 | 0.40 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 529 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 373 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5YS0 · Crystal structure of the second starkin domain of LAM2 in complex with ergosterol · the same entry in another collection · chain A against A, TM-score 1.00
- Q06681 · AlphaFold monomer V2.0 prediction for membrane-anchored lipid-binding protein YSP2… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q06681
- Elsewhere: RCSB PDB 5YS0 · PDBe 5YS0 · UniProt Q06681
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.