2YQ7

Structure of Bcl-xL bound to BimLOCK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Stabilizing the Pro-Apoptotic Bimbh3 Helix (Bimsahb) Does not Necessarily Enhance Affinity or Biological Activity.

Okamoto, T.Zobel, K.Fedorova, A.Quan, C.Yang, H.Fairbrother, W.J.Huang, D.C.S.Smith, B.J.Deshayes, K.Czabotar, P.E.

(2013) ACS Chem Biol 8: 297

  • DOI: 10.1021/cb3005403
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An attractive approach for developing therapeutic peptides is to enhance binding to their targets by stabilizing their α-helical conformation, for example, stabilized BimBH3 peptides (BimSAHB) designed to induce apoptosis. Unexpectedly, we found that ...

    An attractive approach for developing therapeutic peptides is to enhance binding to their targets by stabilizing their α-helical conformation, for example, stabilized BimBH3 peptides (BimSAHB) designed to induce apoptosis. Unexpectedly, we found that such modified peptides have reduced affinity for their targets, the pro-survival Bcl-2 proteins. We attribute this loss in affinity to disruption of a network of stabilizing intramolecular interactions present in the bound state of the native peptide. Altering this network may compromise binding affinity, as in the case of the BimBH3 stapled peptide studied here. Moreover, cells exposed to these peptides do not readily undergo apoptosis, strongly indicating that BimSAHB is not inherently cell permeable.


    Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade, Parkville, Victoria 3052, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 1
A
158Homo sapiensMutation(s): 0 
Gene Names: BCL2L1BCL2LBCLX
Find proteins for Q07817 (Homo sapiens)
Go to UniProtKB:  Q07817
NIH Common Fund Data Resources
PHAROS  Q07817
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 11
B
20Homo sapiensMutation(s): 4 
Gene Names: BCL2L11BIM
Find proteins for O43521 (Homo sapiens)
Go to UniProtKB:  O43521
NIH Common Fund Data Resources
PHAROS  O43521
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.803α = 90
b = 35.223β = 101.12
c = 61.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.3: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations