6DSQ

Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:2ZA2


Literature

Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target.

Novak, W.R.P.West, K.H.J.Kirkman, L.M.D.Brandt, G.S.

(2018) Acta Crystallogr F Struct Biol Commun 74: 664-668

  • DOI: 10.1107/S2053230X18010610
  • Primary Citation of Related Structures:  
    6DSR, 6DSQ, 6DSS

  • PubMed Abstract: 
  • The development of antimalarial drugs remains a public health priority, and the orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound represents an important advance for structure-based drug-design efforts [Tokuoka et al ...

    The development of antimalarial drugs remains a public health priority, and the orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound represents an important advance for structure-based drug-design efforts [Tokuoka et al. (2008), J. Biochem. 143, 69-78]. The complex of the enzyme bound to the substrate OMP (PDB entry 2za1) would be of particular utility in this regard. However, re-refinement of this structure of the Michaelis complex shows that the bound ligand is the product rather than the substrate. Here, the re-refinement of a set of three structures, the apo enzyme and two versions of the product-bound form (PDB entries 2za1, 2za2 and 2za3), is reported. The improved geometry and fit of these structures to the observed electron density will enhance their utility in antimalarial drug design.


    Related Citations: 
    • Structural basis for the decarboxylation of orotidine 5'-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase.
      Tokuoka, K., Kusakari, Y., Krungkrai, S.R., Matsumura, H., Kai, Y., Krungkrai, J., Horii, T., Inoue, T.
      (2008) J Biochem 143: 69

    Organizational Affiliation

    Chemistry Department, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orotidine 5'-monophosphate decarboxylaseA, B323Plasmodium falciparumMutation(s): 0 
Gene Names: ompdc
EC: 4.1.1.23
UniProt
Find proteins for Q8T6J6 (Plasmodium falciparum)
Explore Q8T6J6 
Go to UniProtKB:  Q8T6J6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.812α = 90
b = 201.812β = 90
c = 44.026γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release