MolNFT v1 · #143346 · protein

Ara H 8.01 in complex with epicatechin

6AWV · Ara H 8 allergen: “Ara H 8.01 in complex with epicatechin”. X-ray diffraction, 3 ligands (28E, BEZ, NA), 7 pockets (best druggability 0.83). MolNFT v1 #143346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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.

Pocket	Volume (Å³)	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 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 523 Å² 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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