8TYF

Plasmodium vivax PMV-WM06 inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb8TYF/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., Czabotar, P.E., Cowman, A.F.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.241 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Plasmodium vivax PMX-XX inhibitor complex

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.

Macromolecule Content

• Total Structure Weight: 53.65 kDa 
• Atom Count: 3,338 
• Modelled Residue Count: 400 
• Deposited Residue Count: 461 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasmepsin V	A	461	Plasmodium vivax Sal-1	Mutation(s): 0  Gene Names: PMV, PVX_116695 EC: 3.4.23
UniProt
Find proteins for A5K302 (Plasmodium vivax (strain Salvador I)) Explore A5K302  Go to UniProtKB:  A5K302
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T0F (Subject of Investigation/LOI)	D [auth A]	(2E,4aR,7aS)-6-[(3M)-3-(2-chlorophenyl)pyridin-2-yl]-7a-(2,5-difluorophenyl)-2-imino-3-methyloctahydro-4H-pyrrolo[3,4-d]pyrimidin-4-one C24 H20 Cl F2 N5 O FCCKGIKLSVNPII-MHECFPHRSA-N
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.241 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.72	α = 90
b = 81.85	β = 90
c = 192.876	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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., Czabotar, P.E., 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