MolNFT v1 · #99664 · protein

Crystal structure of ara H 8 with epicatechin bound

4MA6 · Ara H 8 allergen: “Crystal structure of ara H 8 with epicatechin bound”. X-ray diffraction, 2 ligands (28E, NA), 3 pockets (best druggability 0.77). MolNFT v1 #99664 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4MA6
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ara H 8 allergen
UniProt: Q6VT83
Ligands: 28E, NA
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ara H 8 allergen	protein	156	30% helix, 46% strand	Q6VT83

Ligands and binding sites

28E · (2R,3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol · ligand · chains A
NA · Sodium ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	317	0.77	0.88	35	28E
2	417	0.69	0.81	41	empty
3	83	0.38	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 622 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4MA6 · Crystal structure of Ara h 8 with Epicatechin bound · the same entry in another collection · chain B against B, 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 4MA6 · PDBe 4MA6 · UniProt Q6VT83

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