› 3vb3

X-ray diffraction
2.2Å resolution

Crystal structure of SARS-CoV 3C-like protease in apo form

Released:
DOI: 10.2210/pdb3vb3/pdb
PDB entry 3vb3 coloured by chain, front view.
PDB entry 3vb3 coloured by chain, side view.
PDB entry 3vb3 coloured by chain, top view.
Source organism: Severe acute respiratory syndrome-related coronavirus
Primary publication:
Design, synthesis and crystallographic analysis of nitrile-based broad-spectrum peptidomimetic inhibitors for coronavirus 3C-like proteases.
Chuck CP, Chen C, Ke Z, Wan DC, Chow HF, Wong KB
Eur J Med Chem 59 1-6 (2013)
PMID: 23202846

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143077 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3C-like proteinase nsp5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 306 amino acids
Theoretical weight: 33.88 KDa
Source organism: Severe acute respiratory syndrome-related coronavirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C6U8 (Residues: 3241-3546; Coverage: 7%)
Gene name: 1a
Sequence domains: Coronavirus endopeptidase C30
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PEG 1 x PEG
Ligand EDO 7 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 52.434Å b: 96.741Å c: 67.719Å
α: 90° β: 102.73° γ: 90°
R-values:
R R work R free
0.206 0.189 0.231
Expression system: Escherichia coli

Quick links

Citations

16 review citations

From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design.
Hilgenfeld R. (2014)
15 more

5 mentions without citation

Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CLpro).
Han et al. (2022)
4 more