4ZL4

Plasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-842)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for plasmepsin V inhibition that blocks export of malaria proteins to human erythrocytes.

Hodder, A.N.Sleebs, B.E.Czabotar, P.E.Gazdik, M.Xu, Y.O'Neill, M.T.Lopaticki, S.Nebl, T.Triglia, T.Smith, B.J.Lowes, K.Boddey, J.A.Cowman, A.F.

(2015) Nat.Struct.Mol.Biol. 22: 590-596

  • DOI: 10.1038/nsmb.3061

  • PubMed Abstract: 
  • Plasmepsin V, an essential aspartyl protease of malaria parasites, has a key role in the export of effector proteins to parasite-infected erythrocytes. Consequently, it is an important drug target for the two most virulent malaria parasites of humans ...

    Plasmepsin V, an essential aspartyl protease of malaria parasites, has a key role in the export of effector proteins to parasite-infected erythrocytes. Consequently, it is an important drug target for the two most virulent malaria parasites of humans, Plasmodium falciparum and Plasmodium vivax. We developed a potent inhibitor of plasmepsin V, called WEHI-842, which directly mimics the Plasmodium export element (PEXEL). WEHI-842 inhibits recombinant plasmepsin V with a half-maximal inhibitory concentration of 0.2 nM, efficiently blocks protein export and inhibits parasite growth. We obtained the structure of P. vivax plasmepsin V in complex with WEHI-842 to 2.4-Å resolution, which provides an explanation for the strict requirements for substrate and inhibitor binding. The structure characterizes both a plant-like fold and a malaria-specific helix-turn-helix motif that are likely to be important in cleavage of effector substrates for export.


    Organizational Affiliation

    La Trobe Institute for Molecular Science, La Trobe University, Victoria, Australia.,1] Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. [2] Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.,Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartic protease PM5
A, B
444Plasmodium vivaxMutation(s): 0 
Find proteins for Q6PRR9 (Plasmodium vivax)
Go to UniProtKB:  Q6PRR9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4PK
Query on 4PK

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Download CCD File 
A, B
N-[(benzyloxy)carbonyl]-O-carbamimidamido-L-homoseryl-N-{(3S,4S)-3-hydroxy-6-methyl-1-oxo-1-[(2-phenylethyl)amino]heptan-4-yl}-L-valinamide
C34 H51 N7 O7
VAHRPHLZONNTFF-NUISNXNRSA-N
 Ligand Interaction
4PF
Query on 4PF

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Download CCD File 
B
(2R)-1-[(2R)-2-(2-methoxyethoxy)propoxy]propan-2-amine
C9 H21 N O3
QZWPAMVDKNPIHV-RKDXNWHRSA-N
 Ligand Interaction
SO4
Query on SO4

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

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4PKIC50: 0.4 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.994α = 90.00
b = 203.089β = 121.07
c = 82.165γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia637406
National Health and Medical Research Council (Australia)Australia1057960
National Health and Medical Research Council (Australia)Australia1010326
Howard Hughes Medical InstituteUnited States55007645

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Data collection, Derived calculations