6T48

Bovine enterovirus F3 in complex with glutathione and a Cysteinylglycine dipeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glutathione facilitates enterovirus assembly by binding at a druggable pocket.

Duyvesteyn, H.M.E.Ren, J.Walter, T.S.Fry, E.E.Stuart, D.I.

(2020) Commun Biol 3: 9-9

  • DOI: 10.1038/s42003-019-0722-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enteroviruses cause a range of human and animal diseases, some life-threatening, but there remain no licenced anti-enterovirus drugs. However, a benzene-sulfonamide derivative and related compounds have been shown recently to block infection of a ran ...

    Enteroviruses cause a range of human and animal diseases, some life-threatening, but there remain no licenced anti-enterovirus drugs. However, a benzene-sulfonamide derivative and related compounds have been shown recently to block infection of a range of enteroviruses by binding the capsid at a positively-charged surface depression conserved across many enteroviruses. It has also been established that glutathione is essential for the assembly of many enteroviruses, interacting with the capsid proteins to facilitate the formation of the pentameric assembly intermediate, although the mechanism is unknown. Here we show, by high resolution structure analyses of enterovirus F3, that reduced glutathione binds to the same interprotomer pocket as the benzene-sulfonamide derivative. Bound glutathione makes strong interactions with adjacent protomers, thereby explaining the underlying biological role of this druggable binding pocket and delineating the pharmacophore for potential antivirals.


    Organizational Affiliation

    2Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE UK.,1Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
275Enterovirus FMutation(s): 0 
Find proteins for Q2LKZ0 (Enterovirus F)
Go to UniProtKB:  Q2LKZ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP2
B
244Enterovirus FMutation(s): 0 
Find proteins for Q2LKZ0 (Enterovirus F)
Go to UniProtKB:  Q2LKZ0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
243Enterovirus FMutation(s): 0 
Find proteins for Q2LKZ0 (Enterovirus F)
Go to UniProtKB:  Q2LKZ0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
D
71Enterovirus FMutation(s): 0 
Find proteins for Q2LKZ0 (Enterovirus F)
Go to UniProtKB:  Q2LKZ0
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
STE
Query on STE

Download SDF File 
Download CCD File 
A
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
GLY
Query on GLY

Download SDF File 
Download CCD File 
C
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GSH
Query on GSH

Download SDF File 
Download CCD File 
A
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
CYS
Query on CYS

Download SDF File 
Download CCD File 
A
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.200 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 344.000α = 90.00
b = 349.400β = 90.00
c = 352.700γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
CNSphasing
CNSrefinement
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N00065X/1
Wellcome TrustUnited Kingdom101122/Z/13/Z
Wellcome TrustUnited KingdomALR00750

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release