3IL5

Structure of E. faecalis FabH in complex with 2-({4-bromo-3-[(diethylamino)sulfonyl]benzoyl}amino)benzoic acid

• PDB DOI: https://doi.org/10.2210/pdb3IL5/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-06 Released: 2009-08-25 
• Deposition Author(s): Gajiwala, K.S., Margosiak, S., Lu, J., Cortez, J., Su, Y., Nie, Z., Appelt, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.189 

Starting Model: experimental

Literature

Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme.

Gajiwala, K.S., Margosiak, S., Lu, J., Cortez, J., Su, Y., Nie, Z., Appelt, K.

(2009) FEBS Lett 583: 2939-2946

• PubMed: 19665020 
• DOI: https://doi.org/10.1016/j.febslet.2009.08.001
• Primary Citation of Related Structures:  
  3IL3, 3IL4, 3IL5, 3IL6, 3IL7, 3IL9


• PubMed Abstract: 
  

  FabH (beta-ketoacyl-acyl carrier protein synthase III) is unique in that it initiates fatty acid biosynthesis, is inhibited by long-chain fatty acids providing means for feedback control of the process, and dictates the fatty acid profile of the organism by virtue of its substrate specificity. We report the crystal structures of bacterial FabH enzymes from four different pathogenic species: Enterococcus faecalis, Haemophilus influenzae, Staphylococcus aureus and Escherichia coli. Structural data on the enzyme from different species show important differences in the architecture of the substrate-binding sites that parallel the inter-species diversity in the substrate specificities of these enzymes.

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Organizational Affiliation: 

Quorex Pharmaceuticals, Carlsbad, CA 92008, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 152.48 kDa 
• Atom Count: 10,074 
• Modelled Residue Count: 1,279 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3	A, B, C, D	343	Enterococcus faecalis	Mutation(s): 0  Gene Names: EF_2885, fabH EC: 2.3.1.180
UniProt
Find proteins for Q820T1 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q820T1  Go to UniProtKB:  Q820T1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B82	E [auth A], F [auth B], G [auth C], H [auth D]	2-({[4-bromo-3-(diethylsulfamoyl)phenyl]carbonyl}amino)benzoic acid C18 H19 Br N2 O5 S VNOMZKMKBNFCMC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B82	PDBBind:  3IL5	IC50: 1600 (nM) from 1 assay(s)
	BindingDB:  3IL5	IC50: 1600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.260 
• R-Value Work: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.586	α = 90
b = 84.973	β = 98.5
c = 114.39	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Gajiwala, K.S., Margosiak, S., Lu, J., Cortez, J., Su, Y., Nie, Z., Appelt, K.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description