7OFS

Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 4-(2-hydroxyethyl)phenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.

Srinivasan, V.Brognaro, H.Prabhu, P.R.de Souza, E.E.Gunther, S.Reinke, P.Y.A.Lane, T.J.Ginn, H.Han, H.Ewert, W.Sprenger, J.Koua, F.H.M.Falke, S.Werner, N.Andaleeb, H.Ullah, N.Franca, B.A.Wang, M.Barra, A.L.C.Perbandt, M.Schwinzer, M.Schmidt, C.Brings, L.Lorenzen, K.Schubert, R.Machado, R.R.G.Candido, E.D.Oliveira, D.B.L.Durigon, E.L.Niebling, S.Garcia, A.S.Yefanov, O.Lieske, J.Gelisio, L.Domaracky, M.Middendorf, P.Groessler, M.Trost, F.Galchenkova, M.Mashhour, A.R.Saouane, S.Hakanpaa, J.Wolf, M.Alai, M.G.Turk, D.Pearson, A.R.Chapman, H.N.Hinrichs, W.Wrenger, C.Meents, A.Betzel, C.

(2022) Commun Biol 5: 805-805

  • DOI: https://doi.org/10.1038/s42003-022-03737-7
  • Primary Citation of Related Structures:  
    7NFV, 7OFS, 7OFT, 7OFU

  • PubMed Abstract: 

    SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.


  • Organizational Affiliation

    Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. vasundara.srinivasan@chemie.uni-hamburg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease nsp3315Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YRL (Subject of Investigation/LOI)
Query on YRL

Download Ideal Coordinates CCD File 
E [auth A]4-(2-hydroxyethyl)phenol
C8 H10 O2
YCCILVSKPBXVIP-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.402α = 90
b = 82.402β = 90
c = 134.33γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)European UnionEXC 2056 - project ID 390715994
European CommissionEuropean UnionEU project 101003551 - EXSCALATE4CoV (E4C)

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 2.0: 2021-11-24
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 2.1: 2022-09-07
    Changes: Database references
  • Version 2.2: 2024-01-31
    Changes: Data collection, Refinement description