6YJE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Phosphoglycerate Kinase as a potential target for antimalarial therapy

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate kinase416Plasmodium vivaxMutation(s): 0 
Gene Names: PVC01_070025900PVP01_0721000PVT01_070026100
EC: 2.7.2.3
UniProt
Find proteins for A5K6T9 (Plasmodium vivax (strain Salvador I))
Explore A5K6T9 
Go to UniProtKB:  A5K6T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5K6T9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OTQ (Subject of Investigation/LOI)
Query on OTQ

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.962α = 90
b = 81.246β = 90
c = 124.331γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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