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Crystal structure of rice defensin OsAFP1
Analyse Crystal structure of rice defensin OsAFP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LCQ
- Type
- protein
- Length
- 108 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.62
- Source
- Oryza sativa
- Molecule
- Defensin-like protein CAL1
- UniProt
- Q6K209
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · resolution 1.62 · 1 distinct chain · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Defensin-like protein CAL1 | protein | 54 | 19% helix, 39% strand | Q6K209 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.48 | 0.75 | 29 | PO4 |
Interfaces
1 interface between chains.
- A–B · 541 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 Q6K209
- Elsewhere: RCSB PDB 6LCQ · PDBe 6LCQ · UniProt Q6K209
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