2QNZ

Crystal structure of the complex between the mycobacterium beta-ketoacyl-acyl carrier protein synthase III (FABH) and SS-(2-hydroxyethyl)-O-decyl ester carbono(dithioperoxoic) acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Separate Entrance and Exit Portals for Ligand Traffic in Mycobacterium tuberculosis FabH

Sachdeva, S.Musayev, F.N.Alhamadsheh, M.M.Scarsdale, J.N.Wright, H.T.Reynolds, K.A.

(2008) Chem Biol 15: 402-412

  • DOI: 10.1016/j.chembiol.2008.03.007
  • Primary Citation of Related Structures:  
    2QNX, 2QNY, 2QNZ, 2QO0, 2QO1

  • PubMed Abstract: 
  • Mycobacterium tuberculosis FabH initiates type II fatty acid synthase-catalyzed formation of the long chain (C(16)-C(22)) acyl-coenzyme A (CoA) precursors of mycolic acids, which are major constituents of the bacterial cell envelope. Crystal structures of M ...

    Mycobacterium tuberculosis FabH initiates type II fatty acid synthase-catalyzed formation of the long chain (C(16)-C(22)) acyl-coenzyme A (CoA) precursors of mycolic acids, which are major constituents of the bacterial cell envelope. Crystal structures of M. tuberculosis FabH (mtFabH) show the substrate binding site to be a buried, extended L-shaped channel with only a single solvent access portal. Entrance of an acyl-CoA substrate through the solvent portal would require energetically unfavorable reptational threading of the substrate to its reactive position. Using a class of FabH inhibitors, we have tested an alternative hypothesis that FabH exists in an "open" form during substrate binding and product release, and a "closed" form in which catalysis and intermediate steps occur. This hypothesis is supported by mass spectrometric analysis of the product profile and crystal structures of complexes of mtFabH with these inhibitors.


    Related Citations: 
    • Crystal Structure of the Mycobacterium Tuberculosis Beta-Ketoacyl-Acy; Carrier Protein Synthase III
      Scarsdale, J.N., Kazanina, G., He, X., Reynolds, K.A., Wright, H.T.
      (2001) J Biol Chem 276: 20516
    • Crystal Structure of a Substrate Complex of Mycobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Sythnase III (FABH) with Lauroyl-Coenzyme A.
      Musayev, F., Sachdeva, S., Scarsdale, J.N., Reynolds, K.A., Wright, H.T.
      (2005) J Mol Biol 346: 1313

    Organizational Affiliation

    Department of Chemistry, Portland State University, Portland, OR 97207, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase 3A, B335Mycobacterium tuberculosisMutation(s): 0 
Gene Names: fabH
EC: 2.3.1.41 (PDB Primary Data), 2.3.1.180 (UniProt)
UniProt
Find proteins for P9WNG3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNG3 
Go to UniProtKB:  P9WNG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNG3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DFD
Query on DFD

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
DECYL FORMATE
C11 H22 O2
BCLJZFLDSCTULJ-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DFD PDBBind:  2QNZ IC50: 3800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.03α = 90
b = 88.85β = 90
c = 229.74γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance