6YJE | pdb_00006yje

Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEG3350 and ammonium acetate at pH 5.5

• PDB DOI: https://doi.org/10.2210/pdb6YJE/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): Blaszczyk, B.K., Hyvonen, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Phosphoglycerate Kinase as a potential target for antimalarial therapy

Bilsland, E., Costa, F., Blaszczyk, B.K., Hyvonen, M., Sunnerhagen, P.

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: 45.52 kDa 
• Atom Count: 3,567 
• Modeled 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OTQ (Subject of Investigation/LOI)	B [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.962	α = 90
b = 81.246	β = 90
c = 124.331	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

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