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Crystal Structure of Ara h 8 with MES bound

Analyse Crystal Structure of Ara h 8 with MES bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M9W
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.95
Source: Arachis hypogaea
Molecule: Ara h 8 allergen
UniProt: Q6VT83
Ligands: NA
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · resolution 1.95 · 1 distinct chain · 31% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ara h 8 allergen	protein	156	31% helix, 45% strand	Q6VT83

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	156	0.76	0.93	29	MES
2	425	0.74	0.84	41	empty
3	407	0.62	0.77	47	empty
4	53	0.26	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 589 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4M9W · Crystal structure of ara H 8 with mes bound · 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 4M9W · PDBe 4M9W · UniProt Q6VT83

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