Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) at 1.2 A Resolution and a Possible Capture of Zinc Binding Intermediate

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


Drug-Like Compounds as Efficient Covalent Binders of the SARS-CoV-2 Main Protease 3CLPro: Hepatitis C Virus NS3/4A Inhibitors and Others

Andi, B.Kumaran, D.Kreitler, D.F.Soares, A.S.Shi, W.Jakoncic, J.Fuchs, M.R.Keereetaweep, J.Shanklin, J.McSweeney, S.

To be published.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), (UniProt), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.784α = 90
b = 52.931β = 100.07
c = 111.273γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM133893
Department of Energy (DOE, United States)United StatesKP1605010
Brookhaven National Laboratory (BNL)United StatesLDRD 20-042
National Virtual Biotechnology Laboratory (NVBL)United StatesCoronavirus CARES Act

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 2.0: 2022-03-16
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary