› 3e9s

X-ray diffraction
2.5Å resolution

A new class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

Released:
DOI: 10.2210/pdb3e9s/pdb
PDB entry 3e9s coloured by chain, front view.
PDB entry 3e9s coloured by chain, side view.
PDB entry 3e9s coloured by chain, top view.
Source organism: Severe acute respiratory syndrome-related coronavirus
Entry authors: Mesecar AD, Ratia K, Pegan S

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:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143071 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Papain-like protease nsp3 Chain: A
Molecule details ›
Chain: A
Length: 318 amino acids
Theoretical weight: 35.73 KDa
Source organism: Severe acute respiratory syndrome-related coronavirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C6U8 (Residues: 1541-1855; Coverage: 7%)
Gene name: 1a
Sequence domains: Coronavirus papain-like peptidase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand TTT 1 x TTT
Ligand ZN 1 x ZN
Ligand CL 2 x CL
1 modified residue:
Ligand OCS 1 x OCS

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: I222
Unit cell:
a: 71.703Å b: 90.684Å c: 109.537Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.261
Expression system: Escherichia coli

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