› 2h9h

X-ray diffraction
1.39Å resolution

An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors

Released:
DOI: 10.2210/pdb2h9h/pdb
PDB entry 2h9h coloured by chain, front view.
PDB entry 2h9h coloured by chain, side view.
PDB entry 2h9h coloured by chain, top view.
Source organism: Hepatovirus A
Primary publication:
An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors.
Yin J, Cherney MM, Bergmann EM, Zhang J, Huitema C, Pettersson H, Eltis LD, Vederas JC, James MN
OpenAccess logo J Mol Biol 361 673-86 (2006)
PMID: 16860823

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140228 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protease 3C Chain: A
Molecule details ›
Chain: A
Length: 212 amino acids
Theoretical weight: 23.29 KDa
Source organism: Hepatovirus A
Expression system: Escherichia coli
UniProt:
  • Canonical: P08617 (Residues: 1520-1731; Coverage: 10%)
Sequence domains: 3C cysteine protease (picornain 3C)
Structure domains: Trypsin-like serine proteases
Three residue peptide Chain: I
Molecule details ›
Chain: I
Length: 6 amino acids
Theoretical weight: 472 Da
Source organism: Hepatovirus A
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand BBL 1 x BBL
1 modified residue:
Ligand QMM 1 x QMM

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 44.672Å b: 56.055Å c: 80.974Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.181 0.197
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

What coronavirus 3C-like protease tells us: From structure, substrate selectivity, to inhibitor design.
Xiong et al. (2021)
3 more

3 mentions without citation

Crystal structures of enterovirus 71 3C protease complexed with rupintrivir reveal the roles of catalytically important residues.
Wang et al. (2011)
2 more