3ZGC

crystal structure of the KEAP1-NEH2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal-Contact Engineering to Obtain a Crystal Form of the Kelch Domain of Human Keap1 Suitable for Ligand-Soaking Experiments.

Horer, S.Reinert, D.Ostmann, K.Hoevels, Y.Nar, H.

(2013) Acta Crystallogr.,Sect.F 69: 592

  • DOI: 10.1107/S174430911301124X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Keap1 is a substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex and plays an important role in the cellular response to oxidative stress. It binds Nrf2 with its Kelch domain and thus triggers the ubiquitinylation and degradation of ...

    Keap1 is a substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex and plays an important role in the cellular response to oxidative stress. It binds Nrf2 with its Kelch domain and thus triggers the ubiquitinylation and degradation of Nrf2. Oxidative stress prevents the degradation of Nrf2 and leads to the activation of cytoprotective genes. Therefore, Keap1 is an attractive drug target in inflammatory diseases. The support of a medicinal chemistry effort by structural research requires a robust crystallization system in which the crystals are preferably suited for performing soaking experiments. This facilitates the generation of protein-ligand complexes in a routine and high-throughput manner. The structure of human Keap1 has been described previously. In this crystal form, however, the binding site for Nrf2 was blocked by a crystal contact. This interaction was analysed and mutations were introduced to disrupt this crystal contact. One double mutation (E540A/E542A) crystallized in a new crystal form in which the binding site for Nrf2 was not blocked and was accessible to small-molecule ligands. The crystal structures of the apo form of the mutated Keap1 Kelch domain (1.98 Å resolution) and of the complex with an Nrf2-derived peptide obtained by soaking (2.20 Å resolution) are reported.


    Organizational Affiliation

    Department of Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH and Co KG, Birkendorferstrasse 65, 88400 Biberach, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KELCH-LIKE ECH-ASSOCIATED PROTEIN 1
A, B
310Homo sapiensMutation(s): 2 
Gene Names: KEAP1 (INRF2, KIAA0132, KLHL19)
Find proteins for Q14145 (Homo sapiens)
Go to Gene View: KEAP1
Go to UniProtKB:  Q14145
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR FACTOR ERYTHROID 2-RELATED FACTOR 2
C
7Homo sapiensMutation(s): 1 
Gene Names: NFE2L2 (NRF2)
Find proteins for Q16236 (Homo sapiens)
Go to Gene View: NFE2L2
Go to UniProtKB:  Q16236
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.103α = 90.00
b = 76.064β = 90.00
c = 207.541γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Advisory, Data collection, Derived calculations