GH3 exo-beta-xylosidase (xlnd) in complex with xylobiose aziridine activity based probe

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).

Ligands and binding sites

• HLB · 5-[3,3-dimethyl-2-[5-(1,3,3-trimethylindol-2-ylidene) penta-1,3-dienyl]indol-1-ium-1-yl]-~{N}-[8-[[(1~{R}, 2~{S},3~{S},4~{S},5~{R})-2,3,4,5-tetrakis(oxidanyl) cyclohexyl]amino]octyl]pentanamide · ligand · 2 copies · chains B, A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains B, A
• MAN · alpha-D-mannopyranose · sugar · 13 copies · chains B, A
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, A
• EDO · 1,2-ethanediol · additive · 4 copies · chains B, A

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• B–A · 1897 Ų buried · 23 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 6Q7J · GH3 exo-beta-xylosidase (XlnD) in complex with xylobiose aziridine activity based probe · 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 6Q7J · PDBe 6Q7J · UniProt Q5BAS1