1RQC

Crystals of peptide deformylase from Plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An improved crystal form of Plasmodium falciparum peptide deformylase

Robien, M.A.Nguyen, K.T.Kumar, A.Hirsh, I.Turley, S.Pei, D.Hol, W.G.

(2004) Protein Sci 13: 1155-1163

  • DOI: https://doi.org/10.1110/ps.03456404
  • Primary Citation of Related Structures:  
    1RL4, 1RQC

  • PubMed Abstract: 

    An altered version of peptide deformylase from Plasmodium falciparum (PfPDF), the organism that causes the most devastating form of malaria, has been cocrystallized with a synthesized inhibitor that has submicromolar affinity for its target protein. The structure is solved at 2.2 A resolution, an improvement over the 2.8 A resolution achieved during the structural determination of unliganded PfPDF. This represents the successful outcome of modifying the protein construct in order to overcome adverse crystal contacts and other problems encountered in the study of unliganded PfPDF. Two molecules of PfPDF are found in the asymmetric unit of the current structure. The active site of each monomer of PfPDF is occupied by a proteolyzed fragment of the tripeptide-like inhibitor. Unexpectedly, each PfPDF subunit is associated with two nearly complete molecules of the inhibitor, found at a protein-protein interface. This is the first structure of a eukaryotic PDF protein, a potential drug target, in complex with a ligand.


  • Organizational Affiliation

    University of Washington, Seattle, Washington 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
formylmethionine deformylase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
185Plasmodium falciparumMutation(s): 3 
Gene Names: PDF
UniProt
Find proteins for Q8I372 (Plasmodium falciparum (isolate 3D7))
Explore Q8I372 
Go to UniProtKB:  Q8I372
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I372
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.263α = 90
b = 121.263β = 90
c = 177.272γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing
SHARPphasing
DMphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance