Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 33.22 kDa 
• Atom Count: 2406 
• Residue Count: 271 
• Unique protein chains: 1

2W5B

Human Nek2 kinase ATPgammaS-bound

• DOI: 10.2210/pdb2W5B/pdb

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


• Deposited: 2008-12-08 Released: 2008-12-23 
• Deposition Author(s): Bayliss, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Insights Into the Conformational Variability and Regulation of Human Nek2 Kinase.

Westwood, I., Cheary, D.M., Baxter, J.E., Richards, M.W., Van Montfort, R.L., Fry, A.M., Bayliss, R.

(2009) J Mol Biol 386: 476

• PubMed: 19124027 
• DOI: 10.1016/j.jmb.2008.12.033
• Primary Citation of Related Structures:  
  2W5H, 2W5A, 2W5B


• PubMed Abstract: 
  

The Nek family of serine/threonine kinases regulates centrosome and cilia function; in addition, several of its members are potential targets for drug discovery. Nek2 is dimeric, is cell cycle regulated and functions in the separation of centrosomes at G2/M. Here, we report the crystal structures of wild-type human Nek2 kinase domain bound to ADP at 1.55-A resolution and T175A mutant in apo form as well as that bound to a non-hydrolyzable ATP analog. These show that regions of the Nek2 structure around the nucleotide-binding site can adopt several different but well-defined conformations. None of the conformations was the same as that observed for the previously reported inhibitor-bound structure, and the two nucleotides stabilized two conformations. The structures suggest mechanisms for the auto-inhibition of Nek2 that we have tested by mutagenesis. Comparison of the structures with Aurora-A and Cdk2 gives insight into the structural mechanism of Nek2 activation. The production of specific inhibitors that target individual kinases of the human genome is an urgent challenge in drug discovery, and Nek2 is especially promising as a cancer target. We not only identify potential challenges to the task of producing Nek2 inhibitors but also propose that the conformational variability provides an opportunity for the design of Nek2 selective inhibitors because one of the conformations may provide a unique target.

---

Organizational Affiliation: 

The Institute of Cancer Research, London, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE NEK2	A	279	Homo sapiens	Mutation(s): 1  Gene Names: NEK2, NEK2A, NLK1 EC: 2.7.11.1
Find proteins for P51955 (Homo sapiens) Explore P51955  Go to UniProtKB:  P51955
NIH Common Fund Data Resources
PHAROS  P51955 GTEx  ENSG00000117650

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS	A	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.602	α = 90
b = 57.064	β = 133.45
c = 80.802	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-12-08 
• Released Date: 2008-12-23 
Deposition Author(s): Bayliss, R.

Revision History 

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Atomic model, Derived calculations, Non-polymer description, Version format compliance