Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 42400.16 
• Atom Count: 2396 
• Residue Count: 363 
• Unique protein chains: 2

4AF3

Human Aurora B Kinase in complex with INCENP and VX-680

• DOI: 10.2210/pdb4AF3/pdb

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


• Deposited: 2012-01-16 Released: 2012-04-11 
• Deposition Author(s): Elkins, J.M., Vollmar, M., Wang, J., Picaud, S., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 

Literature

Crystal Structure of Human Aurora B in Complex with Incenp and Vx-680.

Elkins, J.M., Santaguida, S., Musacchio, A., Knapp, S.

(2012) J.Med.Chem. 55: 7841

• PubMed: 22920039 
• DOI: 10.1021/jm3008954


• PubMed Abstract: 
  

We present the structure of the human Aurora B kinase domain in complex with the C-terminal Aurora-binding region of human INCENP and the Aurora kinase inhibitor VX-680. The structure unexpectedly reveals a dimeric arrangement of the Aurora B:INCENP complex, which was confirmed to exist in solution by analytical ultracentrifugation. The dimerization involves a domain swap of the activation loop, resulting in a different conformation of the DFG motif as compared to that seen in other kinase complexes with VX-680. The binding of INCENP differs significantly from that seen in the Xenopus laevis Aurora B:INCENP complex currently used as a model for structure-based design for this important oncology target.

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Organizational Affiliation: 

Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
AURORA KINASE B	A	292	Homo sapiens	Mutation(s): 0  Gene Names: AURKB (AIK2, AIM1, AIRK2, ARK2, STK1, STK12, STK5) EC: 2.7.11.1
Find proteins for Q96GD4 (Homo sapiens) Go to Gene View: AURKB Go to UniProtKB:  Q96GD4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
INNER CENTROMERE PROTEIN	D	71	Homo sapiens	Mutation(s): 0  Gene Names: INCENP
Find proteins for Q9NQS7 (Homo sapiens) Go to Gene View: INCENP Go to UniProtKB:  Q9NQS7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
VX6	A	CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE C23 H28 N8 O S GCIKSSRWRFVXBI-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
VX6	Kd: 7 - 7400 nM (99) BINDINGDB
VX6	Ki: 0 - 18 nM (99) BINDINGDB
VX6	IC50: 17 - 55 nM (99) BINDINGDB
VX6	IC50: 31 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.264 
• R-Value Work: 0.205 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 80.145	α = 90.00
b = 80.145	β = 90.00
c = 92.542	γ = 120.00

Software Package:

Software Name	Purpose
SAWAYA	data scaling
XDS	data reduction
PHASER	phasing
REFMAC	refinement
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-16 
• Released Date: 2012-04-11 
• Deposition Author(s): Elkins, J.M., Vollmar, M., Wang, J., Picaud, S., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Knapp, S.

Revision History 

• Version 1.0: 2012-04-11
  Type: Initial release
• Version 1.1: 2012-09-26
  Type: Database references, Structure summary
• Version 1.2: 2018-01-24
  Type: Structure summary