Crystal Structure of Mycobacterium Tuberculosis Shikimate Kinase in Complex with Shikimate and ADP at 2.15 Angstrom Resolution

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.215 

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Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase.

Dhaliwal, B.Nichols, C.E.Ren, J.Lockyer, M.Charles, I.Hawkins, A.R.Stammers, D.K.

(2004) FEBS Lett 574: 49-54

  • DOI: https://doi.org/10.1016/j.febslet.2004.08.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The X-ray crystal structure of Mycobacterium tuberculosis shikimate kinase (SK) with bound shikimate and adenosine diphosphate (ADP) has been determined to a resolution of 2.15 A. The binding of shikimate in a shikimate kinase crystal structure has not previously been reported. The substrate binds in a pocket lined with hydrophobic residues and interacts with several highly conserved charged residues including Asp34, Arg58, Glu61 and Arg136 which project into the cavity. Comparisons of our ternary SK-ADP-shikimate complex with an earlier binary SK-ADP complex show that conformational changes occur on shikimate binding with the substrate-binding domain rotating by 10 degrees. Detailed knowledge of shikimate binding is an important step in the design of inhibitors of SK, which have potential as novel anti-tuberculosis agents.

  • Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Shikimate kinase176Mycobacterium tuberculosisMutation(s): 0 
Gene Names: aroK
Find proteins for P9WPY3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPY3 
Go to UniProtKB:  P9WPY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPY3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.7α = 90
b = 63.7β = 90
c = 91.6γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata 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: 2004-10-19
    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: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description