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 

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:  
  • Also Cited By: 1JYM

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
formylmethionine deformylase
A, B
188Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.5.1.88
Find proteins for Q8I372 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I372
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BL5
Query on BL5

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.197 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 102.317α = 90.00
b = 102.317β = 90.00
c = 118.339γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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