GH3 exo-beta-xylosidase (xlnd)

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains B, A
• MAN · alpha-D-mannopyranose · sugar · 13 copies · chains B, A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, A
• K · Potassium ion · metal · 4 copies · chains B, A
• EDO · 1,2-ethanediol · additive · 11 copies · chains B, A
• GOL · Glycerol · additive · 3 copies · chains B, A
• ACT · Acetate ion · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• B–A · 1926 Ų buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 glycan, 6 disulfide, 2 modified (N-glycosylation, disulfide, cyclization).

Compared structures

• 6Q7I · GH3 exo-beta-xylosidase (XlnD) · the same entry in another collection · chain B against B, TM-score 1.00
• Q5BAS1 · AlphaFold monomer V2.0 prediction for exo-1,4-beta-xylosidase xlnd (Q5BAS1) · a predicted model of the same protein · chain B 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 Q5BAS1
• Elsewhere: RCSB PDB 6Q7I · PDBe 6Q7I · UniProt Q5BAS1