Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) Complexed With An Inhibitor

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.229 

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The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor

Yang, H.Yang, M.Ding, Y.Liu, Y.Lou, Z.Zhou, Z.Sun, L.Mo, L.Ye, S.Pang, H.Gao, G.F.Anand, K.Bartlam, M.Hilgenfeld, R.Rao, Z.

(2003) Proc Natl Acad Sci U S A 100: 13190-13195

  • DOI: https://doi.org/10.1073/pnas.1835675100
  • Primary Citation of Related Structures:  
    1UJ1, 1UK2, 1UK3, 1UK4

  • PubMed Abstract: 

    A newly identified severe acute respiratory syndrome coronavirus (SARS-CoV), is the etiological agent responsible for the outbreak of SARS. The SARS-CoV main protease, which is a 33.8-kDa protease (also called the 3C-like protease), plays a pivotal role in mediating viral replication and transcription functions through extensive proteolytic processing of two replicase polyproteins, pp1a (486 kDa) and pp1ab (790 kDa). Here, we report the crystal structures of the SARS-CoV main protease at different pH values and in complex with a specific inhibitor. The protease structure has a fold that can be described as an augmented serine-protease, but with a Cys-His at the active site. This series of crystal structures, which is the first, to our knowledge, of any protein from the SARS virus, reveal substantial pH-dependent conformational changes, and an unexpected mode of inhibitor binding, providing a structural basis for rational drug design.

  • Organizational Affiliation

    Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, 100084 Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: rep
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
5-mer peptide of inhibitorC [auth G],
D [auth H],
E [auth K]
6synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.633α = 90
b = 97.735β = 102.79
c = 67.931γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 2.0: 2024-01-31
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary