3FDL | pdb_00003fdl

Bim BH3 peptide in complex with Bcl-xL

• PDB DOI: https://doi.org/10.2210/pdb3FDL/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-11-26 Released: 2009-03-10 
• Deposition Author(s): Fairlie, W.D., Lee, E.F., Smith, B.J., Czabotar, P.E., Colman, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

High-Resolution Structural Characterization of a Helical alpha/beta-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-x(L)

Lee, E.F., Sadowsky, J.D., Smith, B.J., Czabotar, P.E., Peterson-Kaufman, K.J., Colman, P.M., Gellman, S.H., Fairlie, W.D.

(2009) Angew Chem Int Ed Engl 48: 4318-4322

• PubMed: 19229915 
• DOI: https://doi.org/10.1002/anie.200805761
• Primary Citation of Related Structures:  
  3FDL, 3FDM


• PubMed Abstract: 
  

  Get into the groove: The first high-resolution structure of a foldamer bound to a protein target is described (see picture; foldamer in sticks). The foldamer consists of alpha- and beta-amino acid residues and is bound to the anti-apoptotic protein Bcl-x(L). The overall binding mode and key interactions observed in the foldamer/Bcl-x(L) complex mimic those seen in complexes of Bcl-x(L) with natural alpha-peptide ligands. Additional contacts in the foldamer/Bcl-x(L) complex involving beta-amino acid residues appear to contribute to binding affinity.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.19 kDa 
• Atom Count: 1,594 
• Modelled Residue Count: 168 
• Deposited Residue Count: 184 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-X	A	158	Homo sapiens	Mutation(s): 0  Gene Names: Bcl-x
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 11	B	26	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens) Explore O43521  Go to UniProtKB:  O43521
PHAROS:  O43521 GTEx:  ENSG00000153094

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.111	α = 90
b = 35.684	β = 111.54
c = 62.76	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Fairlie, W.D., Lee, E.F., Smith, B.J., Czabotar, P.E., Colman, P.M.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-08-16
  Changes: Source and taxonomy
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Refinement description