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Crystal structure of peach pru P3, the prototypic member of the family of plant non-specific lipid transfer protein pan-allergens
Analyse Crystal structure of peach pru P3, the prototypic member of the family of plant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ALG
- Type
- protein
- Length
- 184 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-specific lipid transfer protein
- UniProt
- P81402
- Ligands
- DAO, HP6, SO4
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-specific lipid transfer protein | protein | 92 | 65% helix, 0% strand | P81402 |
Ligands and binding sites
- DAO · Lauric acid · ligand · 2 copies · chains A, B
- HP6 · Heptane · ligand · chains A
- SO4 · Sulfate ion · ion · chains B
- P6G · Hexaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.81 | 0.89 | 39 | DAO, HP6 |
| 2 | 130 | 0.71 | 0.91 | 22 | DAO |
Interfaces
1 interface between chains.
- A–B · 276 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2ALG · Crystal structure of peach Pru p3, the prototypic member of the family of plant… · the same entry in another collection · chain A against A, TM-score 1.00
- P81402 · AlphaFold monomer V2.0 prediction for non-specific lipid-transfer protein 1 (P81402) · 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 P81402
- Elsewhere: RCSB PDB 2ALG · PDBe 2ALG · UniProt P81402
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