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: 32.96 kDa 
• Atom Count: 2183 
• Residue Count: 253 
• Unique protein chains: 1

2JAV

Human Kinase with pyrrole-indolinone ligand

• DOI: 10.2210/pdb2JAV/pdb
• Entry: 2JAV supersedes: 2CL1

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


• Deposited: 2006-11-30 Released: 2006-12-04 
• Deposition Author(s): Pike, A.C.W., Rellos, P., Das, S., Fedorov, O., Papagrigoriou, E., Debreczeni, J.E., Turnbull, A.P., Gorrec, F., Bray, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A., Weigelt, J., von Delft, F., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.277 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Structure and Regulation of the Human Nek2 Centrosomal Kinase

Rellos, P., Ivins, F.J., Baxter, J.E., Pike, A.C.W., Nott, T.J., Parkinson, D.-M., Das, S., Howell, S., Fedorov, O., Shen, Q.Y., Fry, A.M., Knapp, S., Smerdon, S.J.

(2007) J Biol Chem 282: 6833

• PubMed: 17197699 
• DOI: 10.1074/jbc.M609721200
• Primary Citation of Related Structures:  
  2JAV


• PubMed Abstract: 
  

The dimeric Ser/Thr kinase Nek2 regulates centrosome cohesion and separation through phosphorylation of structural components of the centrosome, and aberrant regulation of Nek2 activity can lead to aneuploid defects characteristic of cancer cells. Mutational analysis of autophosphorylation sites within the kinase domain identified by mass spectrometry shows a complex pattern of positive and negative regulatory effects on kinase activity that are correlated with effects on centrosomal splitting efficiency in vivo. The 2.2-A resolution x-ray structure of the Nek2 kinase domain in complex with a pyrrole-indolinone inhibitor reveals an inhibitory helical motif within the activation loop. This helix presents a steric barrier to formation of the active enzyme and generates a surface that may be exploitable in the design of specific inhibitors that selectively target the inactive state. Comparison of this "auto-inhibitory" conformation with similar arrangements in cyclin-dependent kinase 2 and epidermal growth factor receptor kinase suggests a role for dimerization-dependent allosteric regulation that combines with autophosphorylation and protein phosphatase 1c phosphatase activity to generate the precise spatial and temporal control required for Nek2 function in centrosomal maturation.

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Organizational Affiliation: 

Structural Genomics Consortium, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom.

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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5Z5	A	5-[(Z)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE C17 H16 Cl N3 O2 FIRPCWHHIWFKCD-GHXNOFRVSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5Z5	IC50:  8000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.277 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.634	α = 90
b = 56.924	β = 95.98
c = 66.012	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-30 
• Released Date: 2006-12-04 
Deposition Author(s): Pike, A.C.W., Rellos, P., Das, S., Fedorov, O., Papagrigoriou, E., Debreczeni, J.E., Turnbull, A.P., Gorrec, F., Bray, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A., Weigelt, J., von Delft, F., Knapp, S.
• This entry supersedes: 2CL1

Revision History 

• Version 1.0: 2006-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation