6DSS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2ZA3


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: https://doi.org/10.1107/S2053230X18010610
  • Primary Citation of Related Structures:  
    6DSQ, 6DSR, 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. (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.


  • Organizational Affiliation

    Chemistry Department, Wabash College, 301 West Wabash Avenue, Crawfordsville, IN 47933, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orotidine 5'-monophosphate decarboxylase
A, B
323Plasmodium falciparumMutation(s): 0 
Gene Names: ompdc
EC: 4.1.1.23
UniProt
Find proteins for Q8T6J6 (Plasmodium falciparum)
Explore Q8T6J6 
Go to UniProtKB:  Q8T6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8T6J6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.496α = 90
b = 202.496β = 90
c = 44.36γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description