› 4r3d

X-ray diffraction
2.82Å resolution

Crystal structure of MERS Coronavirus papain like protease

Released:
DOI: 10.2210/pdb4r3d/pdb
PDB entry 4r3d coloured by chain, front view.
PDB entry 4r3d coloured by chain, side view.
PDB entry 4r3d coloured by chain, top view.
Source organism: Betacoronavirus England 1
Entry authors: Kong LY, Wang Q, Ming ZH, Shaw N, Sun YN, Yan LM, Lou ZY, Rao ZH

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-125697 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Papain-like protease nsp3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 336 amino acids
Theoretical weight: 37.32 KDa
Source organism: Betacoronavirus England 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: K9N638 (Residues: 1481-1811; Coverage: 8%)
Gene name: 1a
Sequence domains: Coronavirus papain-like peptidase
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: I422
Unit cell:
a: 136.624Å b: 136.624Å c: 239.518Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.224
Expression system: Escherichia coli BL21(DE3)

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