1B07

CRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors.

Nguyen, J.T.Turck, C.W.Cohen, F.E.Zuckermann, R.N.Lim, W.A.

(1998) Science 282: 2088-2092

  • DOI: 10.1126/science.282.5396.2088
  • Primary Citation of Related Structures:  
    3SEM, 2SEM, 1B07

  • PubMed Abstract: 
  • Src homology 3 (SH3) and WW protein interaction domains bind specific proline-rich sequences. However, instead of recognizing critical prolines on the basis of side chain shape or rigidity, these domains broadly accepted amide N-substituted residues. Proline is apparently specifically selected in vivo, despite low complementarity, because it is the only endogenous N-substituted amino acid ...

    Src homology 3 (SH3) and WW protein interaction domains bind specific proline-rich sequences. However, instead of recognizing critical prolines on the basis of side chain shape or rigidity, these domains broadly accepted amide N-substituted residues. Proline is apparently specifically selected in vivo, despite low complementarity, because it is the only endogenous N-substituted amino acid. This discriminatory mechanism explains how these domains achieve specific but low-affinity recognition, a property that is necessary for transient signaling interactions. The mechanism can be exploited: screening a series of ligands in which key prolines were replaced by nonnatural N-substituted residues yielded a ligand that selectively bound the Grb2 SH3 domain with 100 times greater affinity.


    Organizational Affiliation

    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PROTO-ONCOGENE CRK (CRK)) A65Mus musculusMutation(s): 0 
Gene Names: CrkCrko
Find proteins for Q64010 (Mus musculus)
Explore Q64010 
Go to UniProtKB:  Q64010
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SH3 PEPTOID INHIBITOR) C12N/AMutation(s): 0 
Find proteins for Q62245 (Mus musculus)
Explore Q62245 
Go to UniProtKB:  Q62245
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYJ
Query on PYJ

Download Ideal Coordinates CCD File 
C
PHENYLETHANE
C8 H10
YNQLUTRBYVCPMQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.8α = 90
b = 36.8β = 90
c = 52.6γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-12-25
    Changes: Non-polymer description