7TBE

Crystal structure of Plasmepsin X from Plasmodium vivax in complex with WM4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax.

Hodder, A.N.Christensen, J.Scally, S.Triglia, T.Ngo, A.Birkinshaw, R.W.Bailey, B.Favuzza, P.Dietrich, M.H.Tham, W.H.Czabotar, P.E.Lowes, K.Guo, Z.Murgolo, N.Lera Ruiz, M.McCauley, J.A.Sleebs, B.E.Olsen, D.Cowman, A.F.

(2022) Structure 30: 947

  • DOI: https://doi.org/10.1016/j.str.2022.03.018
  • Primary Citation of Related Structures:  
    7TBB, 7TBC, 7TBD, 7TBE

  • PubMed Abstract: 

    Plasmepsins IX (PMIX) and X (PMX) are essential aspartyl proteases for Plasmodium spp. egress, invasion, and development. WM4 and WM382 inhibit PMIX and PMX in Plasmodium falciparum and P. vivax. WM4 inhibits PMX, while WM382 is a dual inhibitor of PMIX and PMX. To understand their function, we identified protein substrates. Enzyme kinetic and structural analyses identified interactions responsible for drug specificity. PMIX and PMX have similar substrate specificity; however, there are distinct differences for peptide and protein substrates. Differences in WM4 and WM382 binding for PMIX and PMX map to variations in the S' region and engagement of the active site S3 pocket. Structures of PMX reveal interactions and mechanistic detail of drug binding important for development of clinical candidates against these targets.


  • Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Parkville 3052 VIC, Australia; University of Melbourne, Melbourne, 3010 VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasmepsin X
A, B, C, D
379Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_010019000PVP01_0112200PVT01_010014800
EC: 3.4.23.1
UniProt
Find proteins for A5KAC3 (Plasmodium vivax (strain Salvador I))
Explore A5KAC3 
Go to UniProtKB:  A5KAC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5KAC3
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.495α = 90
b = 253.278β = 90
c = 171.755γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom109662/Z/15/Z, 202749/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description