3CBX

The Dvl2 PDZ Domain in Complex with the C1 Inhibitory Peptide

• PDB DOI: https://doi.org/10.2210/pdb3CBX/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-02-23 Released: 2009-03-03 
• Deposition Author(s): Appleton, B.A., Wiesmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Inhibition of Wnt signaling by Dishevelled PDZ peptides

Zhang, Y., Appleton, B.A., Wiesmann, C., Lau, T., Costa, M., Hannoush, R.N., Sidhu, S.S.

(2009) Nat Chem Biol 5: 217-219

• PubMed: 19252499 
• DOI: https://doi.org/10.1038/nchembio.152
• Primary Citation of Related Structures:  
  3CBX, 3CBY, 3CBZ, 3CC0


• PubMed Abstract: 
  

  Dishevelled proteins are key regulators of Wnt signaling pathways that have been implicated in the progression of human cancers. We found that the binding cleft of the Dishevelled PDZ domain is more flexible than those of canonical PDZ domains and enables recognition of both C-terminal and internal peptides. These peptide ligands inhibit Wnt/beta-catenin signaling in cells, showing that Dishevelled PDZ domains are potential targets for small-molecule cancer therapeutics.

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Organizational Affiliation: 

Department of Protein Engineering, Genentech, Inc, South San Francisco, California, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.12 kDa 
• Atom Count: 1,724 
• Modelled Residue Count: 204 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dishevelled-2	A, B	105	Homo sapiens	Mutation(s): 1  Gene Names: DVL2
UniProt & NIH Common Fund Data Resources
Find proteins for O14641 (Homo sapiens) Explore O14641  Go to UniProtKB:  O14641
PHAROS:  O14641 GTEx:  ENSG00000004975

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.214	α = 90
b = 61.112	β = 90
c = 65.818	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Appleton, B.A., Wiesmann, C.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description