8TYH

Plasmodium vivax PMX

• PDB DOI: https://doi.org/10.2210/pdb8TYH/pdb

• Classification: HYDROLASE/Inhibitor
• Organism(s): Plasmodium vivax Sal-1
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-08-25 Released: 2024-08-28 
• Deposition Author(s): Hodder, A.N., Scally, S.W., Cowman, A.F.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.251 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Starting Model: experimental

Literature

Plasmodium vivax PMX

Hodder, A.N., Cowman, A.F., Scally, S.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.52 kDa 
• Atom Count: 2,825 
• Modelled Residue Count: 333 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl protease, putative	A	538	Plasmodium vivax Sal-1	Mutation(s): 0  Gene Names: PVX_088125
UniProt
Find proteins for A5KAC3 (Plasmodium vivax (strain Salvador I)) Explore A5KAC3  Go to UniProtKB:  A5KAC3
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TEW	C [auth A]	6-tungstotellurate(VI) O24 Te W6 JDLYBIMRCSJRQJ-UHFFFAOYSA-M
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.251 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.299	α = 90
b = 136.299	β = 90
c = 45.946	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Hodder, A.N., Scally, S.W., Cowman, A.F.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release