trans form of a photoswitchable PDZ domain crosslinked with an azobenzene derivative

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Kinetic response of a photoperturbed allosteric protein.

Buchli, B.Waldauer, S.A.Walser, R.Donten, M.L.Pfister, R.Blochliger, N.Steiner, S.Caflisch, A.Zerbe, O.Hamm, P.

(2013) Proc Natl Acad Sci U S A 110: 11725-11730

  • DOI: https://doi.org/10.1073/pnas.1306323110
  • Primary Citation of Related Structures:  
    2M0Z, 2M10

  • PubMed Abstract: 

    By covalently linking an azobenzene photoswitch across the binding groove of a PDZ domain, a conformational transition, similar to the one occurring upon ligand binding to the unmodified domain, can be initiated on a picosecond timescale by a laser pulse. The protein structures have been characterized in the two photoswitch states through NMR spectroscopy and the transition between them through ultrafast IR spectroscopy and molecular dynamics simulations. The binding groove opens on a 100-ns timescale in a highly nonexponential manner, and the molecular dynamics simulations suggest that the process is governed by the rearrangement of the water network on the protein surface. We propose this rearrangement of the water network to be another possible mechanism of allostery.

  • Organizational Affiliation

    Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 1397Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q12923 (Homo sapiens)
Explore Q12923 
Go to UniProtKB:  Q12923
PHAROS:  Q12923
GTEx:  ENSG00000163629 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12923
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 33B

Download Ideal Coordinates CCD File 
B [auth A]3,3'-(E)-diazene-1,2-diylbis{6-[(chloroacetyl)amino]benzenesulfonic acid}
C16 H14 Cl2 N4 O8 S2
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2013-07-03 
  • Deposition Author(s): Walser, R.

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2013-08-07
    Changes: Database references
  • Version 1.4: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other