Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 68.30 kDa 
• Atom Count: 5099 
• Modelled Residue Count: 570 
• Deposited Residue Count: 620 
• Unique protein chains: 1

3ZGD

crystal structure of a KEAP1 mutant

• DOI: 10.2210/pdb3ZGD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-12-17 Released: 2013-06-12 
• Deposition Author(s): Hoerer, S., Reinert, D., Ostmann, K., Hoevels, Y., Nar, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.181 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

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 Struct Biol Cryst Commun 69: 592

• PubMed: 23722832 
• DOI: 10.1107/S174430911301124X
• Primary Citation of Related Structures:  
  3ZGC, 3ZGD


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KELCH-LIKE ECH-ASSOCIATED PROTEIN 1	A, B	310	Homo sapiens	Mutation(s): 2  Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
Find proteins for Q14145 (Homo sapiens) Explore Q14145  Go to UniProtKB:  Q14145
NIH Common Fund Data Resources
PHAROS:  Q14145 GTEx:  ENSG00000079999

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	A, B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.181 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.72	α = 90
b = 75.77	β = 90
c = 202.04	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
CDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-17 
• Released Date: 2013-06-12 
Deposition Author(s): Hoerer, S., Reinert, D., Ostmann, K., Hoevels, Y., Nar, H.

Revision History  

• Version 1.0: 2013-06-12
  Type: Initial release