4ZL4 | pdb_00004zl4

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 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1038/nsmb.3061
  • Primary Citation Related Structures: 
    4ZL4

  • 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, 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
    • 1] Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. [2] Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.

Macromolecule Content 

  • Total Structure Weight: 103.74 kDa 
  • Atom Count: 6,854 
  • Modeled Residue Count: 790 
  • Deposited Residue Count: 888 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aspartic protease PM5
A, B
444Plasmodium vivaxMutation(s): 0 
EC: 3.4.23
UniProt
Find proteins for A5K302 (Plasmodium vivax (strain Salvador I))
Explore A5K302 
Go to UniProtKB:  A5K302
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K302
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4PK

Query on 4PK



Download:Ideal Coordinates CCD File
C [auth A],
K [auth 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
4PF

Query on 4PF



Download:Ideal Coordinates CCD File
R [auth B](2R)-1-[(2R)-2-(2-methoxyethoxy)propoxy]propan-2-amine
C9 H21 N O3
QZWPAMVDKNPIHV-RKDXNWHRSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
L [auth B]
M [auth B]
D [auth A],
E [auth A],
F [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
P [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4PK BindingDB:  4ZL4 IC50: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.224 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.994α = 90
b = 203.089β = 121.07
c = 82.165γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia637406
National Health and Medical Research Council (NHMRC, Australia)Australia1057960
National Health and Medical Research Council (NHMRC, Australia)Australia1010326
Howard Hughes Medical Institute (HHMI)United States55007645

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-10-23
    Changes: Structure summary