5CFZ | pdb_00005cfz

Crystal structure of E. coli FabI in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.225 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Literature

Crystallographic insights into the structure-activity relationships of diazaborine enoyl-ACP reductase inhibitors.

Jordan, C.A.Sandoval, B.A.Serobyan, M.V.Gilling, D.H.Groziak, M.P.Xu, H.H.Vey, J.L.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1521-1530

  • DOI: https://doi.org/10.1107/S2053230X15022098
  • Primary Citation Related Structures: 
    5CFZ, 5CG1, 5CG2

  • PubMed Abstract: 

    Enoyl-ACP reductase, the last enzyme of the fatty-acid biosynthetic pathway, is the molecular target for several successful antibiotics such as the tuberculosis therapeutic isoniazid. It is currently under investigation as a narrow-spectrum antibiotic target for the treatment of several types of bacterial infections. The diazaborine family is a group of boron heterocycle-based synthetic antibacterial inhibitors known to target enoyl-ACP reductase. Development of this class of molecules has thus far focused solely on the sulfonyl-containing versions. Here, the requirement for the sulfonyl group in the diazaborine scaffold was investigated by examining several recently characterized enoyl-ACP reductase inhibitors that lack the sulfonyl group and exhibit additional variability in substitutions, size and flexibility. Biochemical studies are reported showing the inhibition of Escherichia coli enoyl-ACP reductase by four diazaborines, and the crystal structures of two of the inhibitors bound to E. coli enoyl-ACP reductase solved to 2.07 and 2.11 Å resolution are reported. The results show that the sulfonyl group can be replaced with an amide or thioamide without disruption of the mode of inhibition of the molecule.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330-8262, USA.

Macromolecule Content 

  • Total Structure Weight: 65.38 kDa 
  • Atom Count: 3,879 
  • Modeled Residue Count: 495 
  • Deposited Residue Count: 610 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
A, B
305Escherichia coli K-12Mutation(s): 0 
Gene Names: fabIenvMb1288JW1281
EC: 1.3.1.9
UniProt
Find proteins for P0AEK4 (Escherichia coli (strain K12))
Explore P0AEK4 
Go to UniProtKB:  P0AEK4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEK4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.225 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.152α = 90
b = 80.152β = 90
c = 323.94γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CSUN Faculty DevelopmentUnited StatesProbationary Faculty Support Grant

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description