3FDM

alpha/beta foldamer in complex with Bcl-xL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

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

  • 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 B ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
Apoptosis regulator Bcl-X
A, B, C
158Homo sapiensMutation(s): 0 
Gene Names: BCL2L1 (BCL2L, BCLX)
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
alpha/beta-peptide foldamer
D, E, F
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
D, E, F
NON-POLYMERH2 N

--

XPC
Query on XPC
D, E, F
peptide-likeC5 H10 N2 O2

--

B3L
Query on B3L
D, E, F
L-peptide linkingC7 H15 N O2

--

XCP
Query on XCP
D, E, F
peptide-likeC6 H11 N O2

--

ACE
Query on ACE
D, E, F
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.161α = 90.00
b = 92.281β = 90.00
c = 165.668γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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