Structure of the hemagglutinin-neuraminidase from human parainfluenza virus type III: complex with difluorosialic acid

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).

Ligands and binding sites

• SFJ · (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid · ligand · 3 copies · chains A, B
• FSI · 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · 2 copies · chains A, B
• DF4 · (3R,4R,5R,6R)-5-(acetylamino)-3-fluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]-3,4,5,6-tetrahydropyranium-2-carboxylate · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 13 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1674 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 6 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 4WEF · Structure of the Hemagglutinin-neuraminidase from Human parainfluenza virus type III… · 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 Q6WJ03
• Elsewhere: RCSB PDB 4WEF · PDBe 4WEF · UniProt Q6WJ03