7K3T

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

  • Method: X-RAY DIFFRACTION
  • 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


Literature

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.

Macromolecules
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: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

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