5KNG

CRYSTAL STRUCTURE OF ANTI-IL-13 DARPIN 6G9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational flexibility of an anti-IL-13 DARPin.

Teplyakov, A.Malia, T.J.Obmolova, G.Jacobs, S.A.O'Neil, K.T.Gilliland, G.L.

(2017) Protein Eng. Des. Sel. 30: 31-37

  • DOI: 10.1093/protein/gzw059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Designed ankyrin repeat proteins (DARPin®) are artificial non-immunoglobulin binding proteins with potential applications as therapeutic molecules. DARPin 6G9 binds interleukin-13 with high affinity and blocks the signaling pathway and as such is pro ...

    Designed ankyrin repeat proteins (DARPin®) are artificial non-immunoglobulin binding proteins with potential applications as therapeutic molecules. DARPin 6G9 binds interleukin-13 with high affinity and blocks the signaling pathway and as such is promising for the treatment of asthma and other atopic diseases. The crystal structures of DARPin 6G9 in the unbound form and in complex with IL-13 were determined at high resolution. The DARPin competes for the same epitope as the IL-13 receptor chain 13Rα1 but does not interfere with the binding of the other receptor chain, IL-4Rα. Analysis of multiple copies of the DARPin molecule in the crystal indicates the conformational instability in the N-terminal cap that was predicted from molecular dynamics simulations. Comparison of the DARPin structures in the free state and in complex with IL-13 reveals a concerted movement of the ankyrin repeats upon binding resulted in the opening of the binding site. The induced-fit mode of binding employed by DARPin 6G9 is very unusual for DARPins since they were designed as particularly stable and rigid molecules. This finding shows that DARPins can operate by various binding mechanisms and suggests that some flexibility in the scaffold may be an advantage.


    Organizational Affiliation

    Janssen Research & Development, LLC, 1400 McKean Road, Spring House, PA 19477, USA ateplyak@its.jnj.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DARPIN 6G9
A, B, C, D
169N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 96.080α = 90.00
b = 96.080β = 90.00
c = 206.430γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references