Crystal structure of the papain-like protease of Middle-East Respiratory Syndrome coronavirus

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Crystal structure of the papain-like protease of MERS coronavirus reveals unusual, potentially druggable active-site features.

Lei, J.Mesters, J.R.Drosten, C.Anemuller, S.Ma, Q.Hilgenfeld, R.

(2014) Antiviral Res 109C: 72-82

  • DOI: https://doi.org/10.1016/j.antiviral.2014.06.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Middle-East Respiratory Syndrome coronavirus (MERS-CoV) causes severe acute pneumonia and renal failure. The MERS-CoV papain-like protease (PL(pro)) is a potential target for the development of antiviral drugs. To facilitate these efforts, we determined the three-dimensional structure of the enzyme by X-ray crystallography. The molecule consists of a ubiquitin-like domain and a catalytic core domain. The catalytic domain displays an extended right-hand fold with a zinc ribbon and embraces a solvent-exposed substrate-binding region. The overall structure of the MERS-CoV PL(pro) is similar to that of the corresponding SARS-CoV enzyme, but the architecture of the oxyanion hole and of the S3 as well as the S5 specificity sites differ from the latter. These differences are the likely reason for reduced in vitro peptide hydrolysis and deubiquitinating activities of the MERS-CoV PL(pro), compared to the homologous enzyme from the SARS coronavirus. Introduction of a side-chain capable of oxyanion stabilization through the Leu106Trp mutation greatly enhances the in vitro catalytic activity of the MERS-CoV PL(pro). The unique features observed in the crystal structure of the MERS-CoV PL(pro) should allow the design of antivirals that would not interfere with host ubiquitin-specific proteases.

  • Organizational Affiliation

    Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center for Infection Research (DZIF), Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF1a326Human betacoronavirus 2c EMC/2012Mutation(s): 0 
Gene Names: orf1ab
Find proteins for K0BWD0 (Human betacoronavirus 2c EMC/2012)
Explore K0BWD0 
Go to UniProtKB:  K0BWD0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK0BWD0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CME
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.891α = 90
b = 47.666β = 122.35
c = 88.425γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European CommissionEuropean UnionHEALTH-F3-2010-260644
German Center for Infection Research (DZIF)Germany--
German Research Foundation (DFG)GermanyEXC 306

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-06-04
    Changes: Data collection
  • Version 1.2: 2014-08-06
    Changes: Database references
  • Version 1.3: 2014-08-27
    Changes: Data collection
  • Version 1.4: 2020-01-15
    Changes: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.5: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description