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: 74.73 kDa 
• Atom Count: 5576 
• Residue Count: 616 
• Unique protein chains: 1

4EUU

Structure of BX-795 Complexed with Human TBK1 Kinase Domain Phosphorylated on Ser172

• DOI: 10.2210/pdb4EUU/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-04-25 Released: 2012-05-23 
• Deposition Author(s): Ma, X., Helgason, E., Phung, Q.T., Quan, C.L., Iyer, R.S., Lee, M.W., Bowman, K.K., Starovasnik, M.A., Dueber, E.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Literature

Molecular basis of Tank-binding kinase 1 activation by transautophosphorylation.

Ma, X., Helgason, E., Phung, Q.T., Quan, C.L., Iyer, R.S., Lee, M.W., Bowman, K.K., Starovasnik, M.A., Dueber, E.C.

(2012) Proc Natl Acad Sci U S A 109: 9378-9383

• PubMed: 22619329 
• DOI: 10.1073/pnas.1121552109
• Primary Citation of Related Structures:  
  4EUU, 4EUT


• PubMed Abstract: 
  

Tank-binding kinase (TBK)1 plays a central role in innate immunity: it serves as an integrator of multiple signals induced by receptor-mediated pathogen detection and as a modulator of IFN levels. Efforts to better understand the biology of this key immunological factor have intensified recently as growing evidence implicates aberrant TBK1 activity in a variety of autoimmune diseases and cancers. Nevertheless, key molecular details of TBK1 regulation and substrate selection remain unanswered. Here, structures of phosphorylated and unphosphorylated human TBK1 kinase and ubiquitin-like domains, combined with biochemical studies, indicate a molecular mechanism of activation via transautophosphorylation. These TBK1 structures are consistent with the tripartite architecture observed recently for the related kinase IKKβ, but domain contributions toward target recognition appear to differ for the two enzymes. In particular, both TBK1 autoactivation and substrate specificity are likely driven by signal-dependent colocalization events.

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Organizational Affiliation: 

Departments of Structural Biology, Genentech, South San Francisco, CA 94080, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase TBK1	A, B	319	Homo sapiens	Mutation(s): 1  Gene Names: TBK1, NAK EC: 2.7.11.1
Find proteins for Q9UHD2 (Homo sapiens) Explore Q9UHD2  Go to UniProtKB:  Q9UHD2
NIH Common Fund Data Resources
PHAROS  Q9UHD2 GTEx  ENSG00000183735

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BX7	A, B	N-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide C23 H26 I N7 O2 S VAVXGGRQQJZYBL-UHFFFAOYSA-N
IOD	A, B	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A,B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.194 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.095	α = 90
b = 76.095	β = 90
c = 130.945	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-25 
• Released Date: 2012-05-23 
Deposition Author(s): Ma, X., Helgason, E., Phung, Q.T., Quan, C.L., Iyer, R.S., Lee, M.W., Bowman, K.K., Starovasnik, M.A., Dueber, E.C.

Revision History 

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description