PDBsum entry 1m67

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Oxidoreductase PDB id
Jmol PyMol
Protein chain
346 a.a. *
Waters ×82
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of leishmania mexicana gpdh complexed with 2-bromo-6-hydroxy-purine
Structure: Glycerol-3-phosphate dehydrogenase. Chain: a. Synonym: gpdh, l-glycerol-3-phosphate dehydrogenase. Engineered: yes
Source: Leishmania mexicana. Organism_taxid: 5665. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
2.50Å     R-factor:   0.244     R-free:   0.286
Authors: J.Choe,S.Suresh,G.Wisedchaisri,K.J.Kennedy,M.H.Gelb,W.G.J.Ho
Key ref:
J.Choe et al. (2002). Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase. Chem Biol, 9, 1189-1197. PubMed id: 12445769 DOI: 10.1016/S1074-5521(02)00243-0
12-Jul-02     Release date:   11-Dec-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P90551  (GPDA_LEIME) -  Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal
366 a.a.
346 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glycerol-3-phosphate dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH
sn-glycerol 3-phosphate
+ NAD(+)
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     glycerol-3-phosphate dehydrogenase complex   3 terms 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     4 terms  


DOI no: 10.1016/S1074-5521(02)00243-0 Chem Biol 9:1189-1197 (2002)
PubMed id: 12445769  
Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase.
J.Choe, S.Suresh, G.Wisedchaisri, K.J.Kennedy, M.H.Gelb, W.G.Hol.
Pathogenic protozoa such as Trypanosome and Leishmania species cause tremendous suffering worldwide. Because of their dependence on glycolysis for energy, the glycolytic enzymes of these organisms, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. Using the adenine part of NAD as a lead compound, several 2,6-disubstituted purines were synthesized as inhibitors of Leishmania mexicana GPDH (LmGPDH). The electron densities for the inhibitor 2-bromo-6-chloro-purine bound to LmGPDH using a "conventional" wavelength around 1 A displayed a quasisymmetric shape. The anomalous signals from data collected at 1.77 A clearly indicated the positions of the halogen atoms and revealed the multiple binding modes of this inhibitor. Intriguing differences in the observed binding modes of the inhibitor between very similarly prepared crystals illustrate the possibility of crystal-to-crystal variations in protein-ligand complex structures.
  Selected figure(s)  
Figure 2.
Figure 2. Electron Densities of the Bound Inhibitor BCP(A) Model-unbiased, sigmaA-weighted Fo-Fc map contoured at 3 σ (light brown), 5 σ (violet), and 7 σ (red) with conformation A of BCP.(B and C) Two alternative conformations (conformation A, green; conformation B, red) of BCP bound to L. mexicana GPDH in a model-unbiased, sigmaA-weighted Fo-Fc map (B) contoured at 3.5 σ (light brown) and an anomalous difference Fourier map contoured at 4.5 σ (red) and (C) an anomalous difference Fourier map contoured at 5.5 σ (red). Carbon, nitrogen, chlorine, and bromine are colored brown, blue, yellow, and pink, respectively. Drawn using MOLSCRIPT [45] and Raster3D [46].
Figure 4.
Figure 4. Electron Densities for the Bound Inhibitor BOP(A) Model-unbiased, sigmaA-weighted Fo-Fc map of BOP bound to LmGPDH contoured at 2.4 σ (pink) and the anomalous difference Fourier map (red) contoured at 10 σ superimposed with the final model of BOP.(B) The anomalous difference Fourier map (red) contoured at 10 σ for the whole protein region drawn with the C^α model of the LmGPDH and inhibitor BOP. Carbon, nitrogen, oxygen, and bromine are colored brown, blue, red, and pink, respectively.
  The above figures are reprinted by permission from Cell Press: Chem Biol (2002, 9, 1189-1197) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19536291 F.Ekström, A.Hörnberg, E.Artursson, L.G.Hammarström, G.Schneider, and Y.P.Pang (2009).
Structure of HI-6*sarin-acetylcholinesterase determined by X-ray crystallography and molecular dynamics simulation: reactivator mechanism and design.
  PLoS One, 4, e5957.
PDB codes: 2whp 2whq 2whr
16059670 H.Alonso, M.B.Gillies, P.L.Cummins, A.A.Bliznyuk, and J.E.Gready (2005).
Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase.
  J Comput Aided Mol Des, 19, 165-187.  
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