5MZ7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

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

  • 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 ...

    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

    Present address: Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Disks large homolog 4A, B, C, D101Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4Dlgh4Psd95
Find proteins for P31016 (Rattus norvegicus)
Explore P31016 
Go to UniProtKB:  P31016
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AZH
Query on AZH
A, B, C, DL-PEPTIDE LINKINGC4 H9 N4 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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