2AI8

E.coli Polypeptide Deformylase complexed with SB-485343


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.212 

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This is version 1.3 of the entry. See complete history


Literature

Structural Variation and inhibitor binding in polypeptide deformylase from four different bacterial species.

Smith, K.J.Petit, C.M.Aubart, K.Smyth, M.McManus, E.Jones, J.Fosberry, A.Lewis, C.Lonetto, M.Christensen, S.B.

(2003) Protein Sci 12: 349-360

  • DOI: https://doi.org/10.1110/ps.0229303
  • Primary Citation of Related Structures:  
    2AI7, 2AI8, 2AI9, 2AIA, 2AIE

  • PubMed Abstract: 

    Polypeptide deformylase (PDF) catalyzes the deformylation of polypeptide chains in bacteria. It is essential for bacterial cell viability and is a potential antibacterial drug target. Here, we report the crystal structures of polypeptide deformylase from four different species of bacteria: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Escherichia coli. Comparison of these four structures reveals significant overall differences between the two Gram-negative species (E. coli and H. influenzae) and the two Gram-positive species (S. pneumoniae and S. aureus). Despite these differences and low overall sequence identity, the S1' pocket of PDF is well conserved among the four enzymes studied. We also describe the binding of nonpeptidic inhibitor molecules SB-485345, SB-543668, and SB-505684 to both S. pneumoniae and E. coli PDF. Comparison of these structures shows similar binding interactions with both Gram-negative and Gram-positive species. Understanding the similarities and subtle differences in active site structure between species will help to design broad-spectrum polypeptide deformylase inhibitor molecules.


  • Organizational Affiliation

    GlaxoSmithKline, Harlow, Essex CM19 5AW, UK. Kathrine_J_Smith@gsk.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase
A, B, C
168Escherichia coliMutation(s): 0 
Gene Names: deffms
EC: 3.5.1.88
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Explore P0A6K3 
Go to UniProtKB:  P0A6K3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6K3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.178α = 90
b = 63.35β = 121.23
c = 85.672γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations