PDBe 4mm3

X-ray diffraction
2.75Å resolution

Crystal structure of SARS-CoV papain-like protease PLpro in complex with ubiquitin aldehyde

Released:

Function and Biology Details

Reactions catalysed:
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:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin Chain: A
Molecule details ›
Chain: A
Length: 76 amino acids
Theoretical weight: 8.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Non-structural protein 3 Chain: B
Molecule details ›
Chain: B
Length: 316 amino acids
Theoretical weight: 35.52 KDa
Source organism: SARS coronavirus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0C6U8 (Residues: 1541-1855; Coverage: 7%)
Gene name: 1a
Structure domains:

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P3121
Unit cell:
a: 47.147Å b: 47.147Å c: 332.658Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.192 0.187 0.279
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21(DE3)