6y84

X-ray diffraction
1.39Å resolution

SARS-CoV-2 main protease with unliganded active site (2019-nCoV, coronavirus disease 2019, COVID-19)

Released:
Entry authors: Owen CD, Lukacik P, Strain-Damerell CM, Douangamath A, Powell AJ, Fearon D, Brandao-Neto J, Crawshaw AD, Aragao D, Williams M, Flaig R, Hall DR, McAuley KE, Mazzorana M, Stuart DI, von Delft F, Walsh MA

Function and Biology Details

Reactions catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
ATP + H(2)O = ADP + phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like proteinase Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 33.83 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTD1 (Residues: 3264-3569; Coverage: 4%)
Gene names: 1a-1b, rep

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 112.812Å b: 52.949Å c: 44.631Å
α: 90° β: 103.16° γ: 90°
R-values:
R R work R free
0.179 0.178 0.2
Expression system: Escherichia coli