7jr4

X-ray diffraction
1.55Å resolution

SARS-CoV-2 3CL protease with alternative conformation of the active site promoted by methylene-bridged cysteine and lysine residues

Released:
Entry authors: Nascimento AFZ, de Oliveira RR, Zeri ACM, Trivella DBB

Function and Biology Details

Reactions catalysed:
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
ATP + H(2)O = ADP + phosphate
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).
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
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)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like proteinase nsp5 Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 33.84 KDa
Source organism: Severe acute respiratory syndrome coronavirus 2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DTD1 (Residues: 3264-3569; Coverage: 4%)
Gene names: 1a-1b, rep

Ligands and Environments

1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS SIRUS BEAMLINE MANACA
Spacegroup: C2
Unit cell:
a: 97.153Å b: 82.353Å c: 51.59Å
α: 90° β: 114.62° γ: 90°
R-values:
R R work R free
0.154 0.153 0.18
Expression system: Escherichia coli BL21(DE3)