5C3G

Crystal structure of Bcl-xl bound to BIM-MM

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Hydrocarbon constrained peptides - understanding preorganisation and binding affinity.

Miles, J.A., Yeo, D.J., Rowell, P., Rodriguez-Marin, S., Pask, C.M., Warriner, S.L., Edwards, T.A., Wilson, A.J.

(2016) Chem Sci 7: 3694-3702

  • DOI: 10.1039/c5sc04048e
  • Primary Citation of Related Structures:  
    5C3F, 5C3G

  • PubMed Abstract: 

    • The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-alkenylglycine derived amino acid to synthesise hydrocarbon constrained BH3-family sequences (BIM and BID) ...

    The development of constrained peptides represents an emerging strategy to generate peptide based probes and hits for drug-discovery that address challenging protein-protein interactions (PPIs). In this manuscript we report on the use of a novel α-alkenylglycine derived amino acid to synthesise hydrocarbon constrained BH3-family sequences (BIM and BID). Our biophysical and structural analyses illustrate that whilst the introduction of the constraint increases the population of the bioactive α-helical conformation of the peptide in solution, it does not enhance the inhibitory potency against pro-apoptotic Bcl-x L and Mcl-1 PPIs. SPR analyses indicate binding occurs via an induced fit mechanism whilst X-ray analyses illustrate none of the key interactions between the helix and protein are disturbed. The behaviour derives from enthalpy-entropy compensation which may be considered in terms of the ground state energies of the unbound constrained and unconstrained peptides; this has implications for the design of preorganised peptides to target protein-protein interactions.

    Organizational Affiliation: 

    Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . Email: T.A.Edwards@leeds.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-like protein 1,Bcl-2-like protein 1A153Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07817
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-like protein 11B22Homo sapiensMutation(s): 3 
Gene Names: BCL2L11, BIM
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens)
Explore O43521 
Go to UniProtKB:  O43521
PHAROS:  O43521
GTEx:  ENSG00000153094 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43521
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE		B L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.22α = 90
b = 106.22β = 90
c = 92.76γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
xia2data reduction
xia2data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references