4BPI

Mcl-1 bound to alpha beta Puma BH3 peptide 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.982 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FUSION PROTEIN CONSISTING OF INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 HOMOLOG
A
162Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: MCL1 (BCL2L3), Mcl1
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Find proteins for P97287 (Mus musculus)
Go to UniProtKB:  P97287
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALPHA BETA BH3PEPTIDE
B
19Homo sapiensMutation(s): 0 
Gene Names: BBC3 (PUMA)
Find proteins for Q9BXH1 (Homo sapiens)
Go to Gene View: BBC3
Go to UniProtKB:  Q9BXH1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
B3E
Query on B3E
B
L-PEPTIDE LINKINGC6 H11 N O4GLU
B3A
Query on B3A
B
L-PEPTIDE LINKINGC4 H9 N O2ALA
B3D
Query on B3D
B
PEPTIDE-LIKEC5 H9 N O4ASP
HR7
Query on HR7
B
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
B3Q
Query on B3Q
B
L-peptide linkingC6 H12 N2 O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.982 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.780α = 90.00
b = 53.780β = 90.00
c = 93.965γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-03-15
    Type: Source and taxonomy