Research workbench
X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana
Analyse X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RKN
- Type
- protein
- Length
- 77 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Arabidopsis thaliana
- Molecule
- DIR1 protein
- UniProt
- Q8W453
- Ligands
- LP3, ZN
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 51% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DIR1 protein | protein | 77 | 51% helix, 5% strand | Q8W453 |
Ligands and binding sites
- LP3 · (7R)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacosan-1-aminium 4-oxide · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
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 | 329 | 0.78 | 0.88 | 28 | LP3 |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2RKN · X-ray structure of the self-defense and signaling protein DIR1 from arabidopsis taliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q8W453 · AlphaFold monomer V2.0 prediction for putative lipid-transfer protein DIR1 (Q8W453) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8W453
- Elsewhere: RCSB PDB 2RKN · PDBe 2RKN · UniProt Q8W453
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