Nadase from aspergillus fumigatus with trapped reaction products

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 22% strand (DSSP).

Ligands and binding sites

• NCA · Nicotinamide · ligand · chains A
• AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A
• FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, A
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• PO4 · Phosphate ion · ion · 3 copies · chains B, A
• GOL · Glycerol · additive · 3 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, 4 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• B–A · 2363 Ų buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

• 6YGF · NADase from Aspergillus fumigatus with trapped reaction products · 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 Q4WL81
• Elsewhere: RCSB PDB 6YGF · PDBe 6YGF · UniProt Q4WL81