Crystal Structure of the third PDZ domain from the synaptic protein PSD-95 with incorporated Azidohomoalanine

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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This is version 2.3 of the entry. See complete history


Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding.

Lehner, F.Kudlinzki, D.Richter, C.Muller-Werkmeister, H.M.Eberl, K.B.Bredenbeck, J.Schwalbe, H.Silvers, R.

(2017) Chembiochem 18: 2340-2350

  • DOI: https://doi.org/10.1002/cbic.201700437
  • Primary Citation of Related Structures:  
    5MZ7, 5W72

  • PubMed Abstract: 

    The impact of the incorporation of a non-natural amino acid (NNAA) on protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro through click chemistry. Herein, structural characterisation of the impact of the incorporation of azidohomoalanine (AZH) into the model protein domain PDZ3 is examined by means of NMR spectroscopy and X-ray crystallography. The structure and dynamics of the apo state of AZH-modified PDZ3 remain mostly unperturbed. Furthermore, the binding of two PDZ3 binding peptides are unchanged upon incorporation of AZH. The interface of the AZH-modified PDZ3 and an azulene-linked peptide for vibrational energy transfer studies has been mapped by means of chemical shift perturbations and NOEs between the unlabelled azulene-linked peptide and the isotopically labelled protein. Co-crystallisation and soaking failed for the peptide-bound holo complex. NMR spectroscopy, however, allowed determination of the protein-ligand interface. Although the incorporation of AZH was minimally invasive for PDZ3, structural analysis of NNAA-modified proteins through the methodology presented herein should be performed to ensure structural integrity of the studied target.

  • Organizational Affiliation

    Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disks large homolog 4
A, B, C, D
101Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4Dlgh4Psd95
Find proteins for P31016 (Rattus norvegicus)
Explore P31016 
Go to UniProtKB:  P31016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31016
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on AZH
A, B, C, D
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.207α = 90
b = 34.078β = 101.4
c = 72.244γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Database references
  • Version 1.3: 2017-12-13
    Changes: Database references
  • Version 2.0: 2019-04-24
    Changes: Data collection, Polymer sequence
  • Version 2.1: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 2.2: 2019-10-16
    Changes: Data collection
  • Version 2.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description