Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir octanoate

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).

Ligands and binding sites

• LVO · 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-methyl-9-O-octanoyl-D-glycero-D-galacto-non-2-enonic acid · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, C, B, D
• BMA · beta-D-mannopyranose · sugar · 4 copies · chains C, D, B, A
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, D, B, A
• CA · Calcium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–C · 1669 Ų buried · 33 hydrogen bonds · protein-protein
• A–D · 1667 Ų buried · 31 hydrogen bonds · protein-protein
• B–D · 1667 Ų buried · 32 hydrogen bonds · protein-protein
• B–C · 1663 Ų buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

• 3TIB · Crystal structure of 1957 pandemic H2N2 neuraminidase complexed with laninamivir octanoate · 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 Q194T1
• Elsewhere: RCSB PDB 3TIB · PDBe 3TIB · UniProt Q194T1