Biological Assembly 1  

 3D View: Structure | Electron Density

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Protein Workshop | Ligand Explorer

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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Protein Workshop | Ligand Explorer

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21192.65 
• Atom Count: 1385 
• Residue Count: 184 
• Unique protein chains: 2

3FDL

Bim BH3 peptide in complex with Bcl-xL

• DOI: 10.2210/pdb3FDL/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• 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 
• R-Value Work: 0.160 

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: 10.1002/anie.200805761
• Primary Citation of Related Structures:  
  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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Apoptosis regulator Bcl-X	A	158	Homo sapiens	Gene Names: BCL2L1 (BCL2L, BCLX)
Find proteins for Q07817 (Homo sapiens) Go to Gene View: BCL2L1 Go to UniProtKB:  Q07817

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Bcl-2-like protein 11	B	26	Homo sapiens	Gene Names: BCL2L11 (BIM)
Find proteins for O43521 (Homo sapiens) Go to Gene View: BCL2L11 Go to UniProtKB:  O43521

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.208 
• R-Value Work: 0.160 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 74.111	α = 90.00
b = 35.684	β = 111.54
c = 62.760	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-26 
• 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
  Type: Version format compliance
• Version 1.2: 2017-08-09
  Type: Refinement description, Source and taxonomy
• Version 1.3: 2017-08-16
  Type: Source and taxonomy