1YWG

The structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum.

Satchell, J.F.Malby, R.L.Luo, C.S.Adisa, A.Alpyurek, A.E.Klonis, N.Smith, B.J.Tilley, L.Colman, P.M.

(2005) Acta Crystallogr.,Sect.D 61: 1213-1221

  • DOI: 10.1107/S0907444905018317

  • PubMed Abstract: 
  • The malaria parasite Plasmodium falciparum is responsible for about two million deaths annually, making it important to obtain information about enzymes from this organism that represent potential drug targets. The gene for P. falciparum glyceraldehy ...

    The malaria parasite Plasmodium falciparum is responsible for about two million deaths annually, making it important to obtain information about enzymes from this organism that represent potential drug targets. The gene for P. falciparum glyceraldehyde-3-phosphate dehydrogenase (PfGAPDH) has been cloned and the protein expressed as a hexahistidine-tagged recombinant protein in Escherichia coli. The recombinant protein has been crystallized and its three-dimensional structure determined. One molecule of the cofactor NAD+ is bound to each of the four subunits in the tetrameric enzyme. The major structural feature distinguishing human GAPDH from PfGAPDH is the insertion of a dipeptide (-KG-) in the so-called S loop. This insert, together with other characteristic single-amino-acid substitutions, alters the chemical environment of the groove that encompasses the R dyad and that links adjacent cofactor-binding sites and may be responsible for the selective inhibition of the enzyme by ferriprotoporphyrin IX.


    Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glyceraldehyde-3-phosphate dehydrogenase
O, P, Q, R
337Plasmodium falciparumEC: 1.2.1.12
Find proteins for Q8T6B1 (Plasmodium falciparum)
Go to UniProtKB:  Q8T6B1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
O, P, Q, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.231 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 79.600α = 90.00
b = 79.600β = 90.00
c = 406.300γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-11-12
    Type: Structure summary