Research workbench
Ara H 8.01 in complex with epicatechin
Analyse Ara H 8.01 in complex with epicatechin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AWV
- Type
- protein
- Length
- 467 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ara H 8 allergen
- UniProt
- Q6VT83
- Ligands
- 28E, BEZ, NA
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ara H 8 allergen | protein | 156 | 28% helix, 46% strand | Q6VT83 |
| B | Ara H 8 allergen | protein | 155 | 30% helix, 45% strand | Q6VT83 |
Ligands and binding sites
- 28E · (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol · ligand · 4 copies · chains A, B, C
- BEZ · Benzoic acid · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.83 | 0.87 | 67 | 28E |
| 2 | 417 | 0.73 | 0.83 | 42 | 28E |
| 3 | 342 | 0.64 | 0.79 | 45 | 28E |
| 4 | 57 | 0.52 | 0.87 | 17 | BEZ |
| 5 | 169 | 0.51 | 0.77 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–C · 650 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 523 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6AWV · Ara h 8.01 in complex with epicatechin · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6VT83
- Elsewhere: RCSB PDB 6AWV · PDBe 6AWV · UniProt Q6VT83
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