5VWZ

Bak in complex with Bim-h3Pc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.622 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design.

Brouwer, J.M.Lan, P.Cowan, A.D.Bernardini, J.P.Birkinshaw, R.W.van Delft, M.F.Sleebs, B.E.Robin, A.Y.Wardak, A.Tan, I.K.Reljic, B.Lee, E.F.Fairlie, W.D.Call, M.J.Smith, B.J.Dewson, G.Lessene, G.Colman, P.M.Czabotar, P.E.

(2017) Mol. Cell 68: 659-672.e9

  • DOI: 10.1016/j.molcel.2017.11.001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Certain BH3-only proteins transiently bind and activate Bak and Bax, initiating their oligomerization and the permeabilization of the mitochondrial outer membrane, a pivotal step in the mitochondrial pathway to apoptosis. Here we describe the first c ...

    Certain BH3-only proteins transiently bind and activate Bak and Bax, initiating their oligomerization and the permeabilization of the mitochondrial outer membrane, a pivotal step in the mitochondrial pathway to apoptosis. Here we describe the first crystal structures of an activator BH3 peptide bound to Bak and illustrate their use in the design of BH3 derivatives capable of inhibiting human Bak on mitochondria. These BH3 derivatives compete for the activation site at the canonical groove, are the first engineered inhibitors of Bak activation, and support the role of key conformational transitions associated with Bak activation.


    Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bcl-2 homologous antagonist/killer
A, C
170Homo sapiensMutation(s): 1 
Gene Names: BAK1 (BAK, BCL2L7, CDN1)
Find proteins for Q16611 (Homo sapiens)
Go to Gene View: BAK1
Go to UniProtKB:  Q16611
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bcl-2-like protein 11
B, D
26Homo sapiensMutation(s): 0 
Gene Names: BCL2L11 (BIM)
Find proteins for O43521 (Homo sapiens)
Go to Gene View: BCL2L11
Go to UniProtKB:  O43521
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

Download SDF File 
Download CCD File 
C
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
D
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
9R1
Query on 9R1
B, D
L-peptide linkingC8 H15 N O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.622 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.237α = 90.00
b = 56.668β = 103.32
c = 79.291γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata processing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia1079706
National Health and Medical Research Council (Australia)Australia1058331
National Health and Medical Research Council (Australia)Australia1113133

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references