6YJF

Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEGSmear at pH 6.5

• PDB DOI: https://doi.org/10.2210/pdb6YJF/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Plasmodium vivax
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-03 Released: 2021-04-14 
• Deposition Author(s): Hyvonen, M., Brear, P., Blaszczyk, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Phosphoglycerate Kinase as a potential target for antimalarial therapy

King, L., Brear, P., Bourgard, C., Cassiano, C., Mota, D., Blaszczyk, B.K., Tomaz, K., Khedim, M., Furlan, M., Ramos, P., Andresen, E., Tarczykowska, A., Tiburcio, L., Kurowska, A., Sulskis, D., Oliver, S., Grotli, M., Massirer, K., Saphire, E., Burmann, B., Witkowski, B., Costa, F., Sunnerhagen, P., Hyvonen, M., Bilsland, E.

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: 45.61 kDa 
• Atom Count: 3,485 
• Modelled Residue Count: 416 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate kinase	A	416	Plasmodium vivax	Mutation(s): 0  Gene Names: PVC01_070025900, PVP01_0721000, PVT01_070026100 EC: 2.7.2.3
UniProt
Find proteins for A5K6T9 (Plasmodium vivax (strain Salvador I)) Explore A5K6T9  Go to UniProtKB:  A5K6T9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OTQ (Subject of Investigation/LOI)	C [auth A]	(2~{S})-2-(5-nitrofuran-2-yl)-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one C14 H13 N3 O4 S MOKSPNCNIWVHBB-LBPRGKRZSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.594	α = 90
b = 82.315	β = 90
c = 124.495	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Hyvonen, M., Brear, P., Blaszczyk, B.K.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 2.0: 2022-05-11
  Changes: Database references, Non-polymer description, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Refinement description