› 4zro

X-ray diffraction
2.06Å resolution

2.1 A X-Ray Structure of FIPV-3CLpro bound to covalent inhibitor

Released:
DOI: 10.2210/pdb4zro/pdb
PDB entry 4zro coloured by chain, front view.
PDB entry 4zro coloured by chain, side view.
PDB entry 4zro coloured by chain, top view.
Source organisms:
Primary publication:
X-ray structure and inhibition of the feline infectious peritonitis virus 3C-like protease: Structural implications for drug design.
St John SE, Therkelsen MD, Nyalapatla PR, Osswald HL, Ghosh AK, Mesecar AD
Bioorg Med Chem Lett 25 5072-7 (2015)
PMID: 26592814

Function and Biology Details

Reactions catalysed: 
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]
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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).
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165411 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
3C-like proteinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 299 amino acids
Theoretical weight: 32.73 KDa
Source organism: Feline infectious peritonitis virus (strain 79-1146)
Expression system: Escherichia coli
UniProt:
  • Canonical: Q98VG9 (Residues: 2904-3202; Coverage: 5%)
Gene names: 1a-1b, rep
Sequence domains: Coronavirus endopeptidase C30
Structure domains:
Bounded inhibitor of N-(tert-butoxycarbonyl)-L-seryl-L-valyl-N-{(2S)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-leucinamide Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 5 amino acids
Theoretical weight: 628 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand DMS 2 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 100.449Å b: 101.896Å c: 110.158Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.231
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Drug Development and Medicinal Chemistry Efforts toward SARS-Coronavirus and Covid-19 Therapeutics.
Ghosh et al. (2020)
1 more

13 mentions without citation

What coronavirus 3C-like protease tells us: From structure, substrate selectivity, to inhibitor design.
Xiong et al. (2021)
12 more