2A94

Structure of Plasmodium falciparum lactate dehydrogenase complexed to APADH.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Lactate Dehydrogenase from Plasmodium vivax: Complexes with NADH and APADH.

Chaikuad, A.Fairweather, V.Conners, R.Joseph-Horne, T.Turgut-Balik, D.Brady, R.L.

(2005) Biochemistry 44: 16221-16228

  • DOI: 10.1021/bi051416y
  • Primary Citation of Related Structures:  
    2A94, 2A92, 2AA3

  • PubMed Abstract: 
  • Malaria caused by Plasmodium vivax is a major cause of global morbidity and, in rare cases, mortality. Lactate dehydrogenase is an essential Plasmodium protein and, therefore, a potential antimalarial drug target. Ideally, drugs directed against this target would be effective against both major species of Plasmodium, P ...

    Malaria caused by Plasmodium vivax is a major cause of global morbidity and, in rare cases, mortality. Lactate dehydrogenase is an essential Plasmodium protein and, therefore, a potential antimalarial drug target. Ideally, drugs directed against this target would be effective against both major species of Plasmodium, P. falciparum and P. vivax. In this study, the crystal structure of the lactate dehydrogenase protein from P. vivax has been solved and is compared to the equivalent structure from the P. falciparum enzyme. The active sites and cofactor binding pockets of both enzymes are found to be highly similar and differentiate these enzymes from their human counterparts. These structures suggest effective inhibition of both enzymes should be readily achievable with a common inhibitor. The crystal structures of both enzymes have also been solved in complex with the synthetic cofactor APADH. The unusual cofactor binding site in these Plasmodium enzymes is found to readily accommodate both NADH and APADH, explaining why the Plasmodium enzymes retain enzymatic activity in the presence of this synthetic cofactor.


    Organizational Affiliation

    Department of Biochemistry, University of Bristol, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-lactate dehydrogenaseA321Plasmodium falciparumMutation(s): 0 
Gene Names: LDH
EC: 1.1.1.27
UniProt
Find proteins for Q27743 (Plasmodium falciparum (isolate CDC / Honduras))
Explore Q27743 
Go to UniProtKB:  Q27743
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AP0
Query on AP0

Download Ideal Coordinates CCD File 
B [auth A]ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED
C22 H32 N6 O14 P2
APPJAZKWQWZFMO-GKIAYCOLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.183α = 90
b = 86.208β = 90
c = 90.826γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description