4BPK

Bcl-xL bound to alpha beta Puma BH3 peptide 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity for Bcl-2 Family Prosurvival Proteins.

Smith, B.J.Lee, E.F.Checco, J.W.Evangelista, M.Gellman, S.H.Fairlie, W.D.

(2013) Chembiochem 14: 1564

  • DOI: 10.1002/cbic.201300351
  • Primary Citation of Related Structures:  
    4BPJ, 4BPK, 4BPI

  • PubMed Abstract: 
  • We have used computational methods to improve the affinity of a foldamer ligand for its target protein. The effort began with a previously reported α/β-peptide based on the BH3 domain of the proapoptotic protein Puma; this foldamer binds tightly to B ...

    We have used computational methods to improve the affinity of a foldamer ligand for its target protein. The effort began with a previously reported α/β-peptide based on the BH3 domain of the proapoptotic protein Puma; this foldamer binds tightly to Bcl-x(L) but weakly to Mcl-1. The crystal structure of the Puma-derived α/β-peptide complexed to Bcl-x(L) was used as the basis for computational design of variants intended to display improved binding to Mcl-1. Molecular modelling suggested modification of three α residues of the original α/β backbone. Individually, each substitution caused only a modest (4- to 15-fold) gain in affinity; however, together the three substitutions led to a 250-fold increase in binding to Mcl-1. These modifications had very little effect on affinity for Bcl-x(L). Crystal structures of a number of the new α/β-peptides bound to either Mcl-1 or Bcl-x(L) validated the selection of each substitution. Overall, our findings demonstrate that structure-guided rational design can be used to improve affinity and alter partner selectivity of peptidic ligands with unnatural backbones that bind to specific protein partners.


    Organizational Affiliation

    Department of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria (Australia). brian.smith@latrobe.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BCL-2-LIKE PROTEIN 1AB157Homo sapiensMutation(s): 0 
Gene Names: BCL2L1BCL2LBCLX
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
NIH Common Fund Data Resources
PHAROS  Q07817
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA BETA BH3-PEPTIDECD22Homo sapiensMutation(s): 0 
Gene Names: BBC3PUMA
Find proteins for Q9BXH1 (Homo sapiens)
Explore Q9BXH1 
Go to UniProtKB:  Q9BXH1
NIH Common Fund Data Resources
PHAROS  Q9BXH1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
AHP
Query on AHP
C,DL-PEPTIDE LINKINGC7 H15 N O2ALA
B3A
Query on B3A
C,DL-PEPTIDE LINKINGC4 H9 N O2ALA
B3D
Query on B3D
C,DPEPTIDE-LIKEC5 H9 N O4ASP
B3E
Query on B3E
C,DL-PEPTIDE LINKINGC6 H11 N O4GLU
HR7
Query on HR7
C,DL-PEPTIDE LINKINGC7 H16 N4 O2ARG
HT7
Query on HT7
C,DL-PEPTIDE LINKINGC12 H14 N2 O2TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.175α = 90
b = 72.133β = 90
c = 80.579γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Data collection
  • Version 2.0: 2018-06-20
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.0: 2019-04-24
    Changes: Data collection, Polymer sequence
  • Version 3.1: 2019-07-10
    Changes: Data collection