› 4h53

X-ray diffraction
1.5Å resolution

Influenza N2-Tyr406Asp neuraminidase in complex with beta-Neu5Ac

Released:
DOI: 10.2210/pdb4h53/pdb
PDB entry 4h53 coloured by chain, front view.
PDB entry 4h53 coloured by chain, side view.
PDB entry 4h53 coloured by chain, top view.
Source organism: Influenza A virus (A/RI/5+/1957(H2N2))
Primary publication:
Influenza neuraminidase operates via a nucleophilic mechanism and can be targeted by covalent inhibitors.
Vavricka CJ, Liu Y, Kiyota H, Sriwilaijaroen N, Qi J, Tanaka K, Wu Y, Li Q, Li Y, Yan J, Suzuki Y, Gao GF
Nat Commun 4 1491 (2013)
PMID: 23422659

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172754 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (6 distinct):
Neuraminidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 388 amino acids
Theoretical weight: 43.01 KDa
Source organism: Influenza A virus (A/RI/5+/1957(H2N2))
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q194T1 (Residues: 82-469; Coverage: 83%)
Gene name: NA
Sequence domains: Neuraminidase
Structure domains: Neuraminidase

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: GAL, SIA
Carbohydrate polymer
4 bound ligands:
Ligand CA 3 x CA
Ligand NAG 1 x NAG
Ligand SLB 3 x SLB
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 83.217Å b: 114.831Å c: 84.259Å
α: 90° β: 99.71° γ: 90°
R-values:
R R work R free
0.161 0.14 0.161
Expression system: Spodoptera frugiperda

Quick links

Citations

12 review citations

Influenza Virus Neuraminidase Structure and Functions.
McAuley et al. (2019)
11 more

5 mentions without citation

Influenza A Virus Hemagglutinin-Neuraminidase-Receptor Balance: Preserving Virus Motility.
de Vries et al. (2020)
4 more