5JEX

Crystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in imidazole buffer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A unique peptide deformylase platform to rationally design and challenge novel active compounds.

Fieulaine, S.Alves de Sousa, R.Maigre, L.Hamiche, K.Alimi, M.Bolla, J.M.Taleb, A.Denis, A.Pages, J.M.Artaud, I.Meinnel, T.Giglione, C.

(2016) Sci Rep 6: 35429-35429

  • DOI: 10.1038/srep35429
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae ...

    Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae PDF could be used as PDF prototype as it allowed to get complete sets of 3-dimensional, biophysical and kinetic data with virtually any inhibitor compound. Structure-activity relationship analysis with this single reference system allowed us to reveal distinct binding modes for different PDF inhibitors and the key role of a hydrogen bond in potentiating the interaction between ligand and target. We propose this protein as an irreplaceable tool, allowing easy and relevant fine comparisons between series, to design, challenge and validate novel series of inhibitors. As proof-of-concept, we report here the design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug resistant clinical isolate.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
A
204Streptococcus agalactiae serotype III (strain NEM316)Mutation(s): 1 
Gene Names: def
EC: 3.5.1.88
Find proteins for Q8E378 (Streptococcus agalactiae serotype III (strain NEM316))
Go to UniProtKB:  Q8E378
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.320α = 90.00
b = 65.550β = 90.00
c = 88.710γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
FRODOmodel building
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR6MIME 2006

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence
  • Version 1.2: 2018-04-25
    Type: Data collection
  • Version 1.3: 2018-11-21
    Type: Data collection