6WX4

Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR251


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report



Literature

Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design

Rut, W.Lv, Z.Zmudzinski, M.Patchett, S.Nayak, D.Snipas, S.J.El Oualid, F.Huang, T.T.Bekes, M.Drag, M.Olsen, S.K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-structural protein 3
D
326Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (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)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Go to UniProtKB:  P0DTD1
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VIR251
I
5saltans groupMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002390
Query on PRD_002390
IPapain-like protease peptide inhibitor VIR251Peptide-like /  Enzyme inhibitor

--

Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
73O
Query on 73O
I
L-PEPTIDE LINKINGC10 H13 N O3TYR
DPP
Query on DPP
I
L-PEPTIDE LINKINGC3 H8 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.869α = 90
b = 113.482β = 90
c = 151.048γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-05-09 
  • Released Date: 2020-05-20 
  • Deposition Author(s): Lv, Z., Olsen, S.K.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115568-05

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release