1RL4

Plasmodium falciparum peptide deformylase complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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.J.

(2004) Protein Sci 13: 1155-1163

  • DOI: 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. ...

    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.


    Related Citations: 
    • Crystals of Peptide Deformylase from Plasmodium falciparum Reveal Critical Characteristics of the Active Site for Drug Design
      Kumar, A., Nguyen, K.T., Srivathsan, S., Ornstein, B., Turley, S., Hirsh, I., Pei, D., Hol, W.G.J.
      (2002) Structure 10: 357

    Organizational Affiliation

    University of Washington, Seattle, Washington 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
formylmethionine deformylaseA, B188Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PDFPF3D7_0907900
EC: 3.5.1.31 (PDB Primary Data), 3.5.1.88 (UniProt)
Find proteins for Q8I372 (Plasmodium falciparum (isolate 3D7))
Explore Q8I372 
Go to UniProtKB:  Q8I372
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BL5
Query on BL5

Download CCD File 
A, B
2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE
C38 H62 N8 O4
YFMXWONORHSZEM-ANFUHZJESA-N
 Ligand Interaction
BRR
Query on BRR

Download CCD File 
A, B
(2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID
C8 H15 N O4
NOSUUIPGNMAALM-SSDOTTSWSA-N
 Ligand Interaction
CO
Query on CO

Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BL5IC50:  130   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.317α = 90
b = 102.317β = 90
c = 118.339γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance