8TYG

Plasmodium vivax PMV-WM08 inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb8TYG/pdb

• Classification: HYDROLASE
• 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: 1.64 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Plasmodium vivax PMV-WM08 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 and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.75 kDa 
• Atom Count: 3,753 
• Modelled Residue Count: 405 
• 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: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TEW	D [auth A]	6-tungstotellurate(VI) O24 Te W6 JDLYBIMRCSJRQJ-UHFFFAOYSA-M
SKC (Subject of Investigation/LOI)	C [auth A]	(2E,4aR,7aS)-6-[3-(4-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 JZQJSLYBFWXABF-YADARESESA-N
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.211 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.772	α = 90
b = 86.994	β = 90
c = 192.463	γ = 90

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