8ykj

X-ray diffraction
1.99Å resolution

Crystal structure of SARS-Cov-2 main protease in complex with X77

Released:

Function and Biology Details

Reactions catalysed:
GTP + a 5'-diphospho-[mRNA] = diphosphate + a 5'-(5'-triphosphoguanosine)-[mRNA]
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.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
PDBe Complex ID:
PDB-CPX-144140 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like proteinase nsp5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 301 amino acids
Theoretical weight: 33.31 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTC1 (Residues: 3266-3566; Coverage: 7%)
Sequence domains: Coronavirus endopeptidase C30

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL02U1
Spacegroup: P212121
Unit cell:
a: 104.414Å b: 67.768Å c: 101.13Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.212 0.252
Expression system: Escherichia coli BL21(DE3)