3EH9

Crystal structure of death associated protein kinase complexed with ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural insight into nucleotide recognition by human death-associated protein kinase.

McNamara, L.K., Watterson, D.M., Brunzelle, J.S.

(2009) Acta Crystallogr D Biol Crystallogr 65: 241-248

  • DOI: 10.1107/S0907444908043679
  • Primary Citation of Related Structures:  
    3EHA, 3EH9, 3F5U, 3F5G

  • PubMed Abstract: 

    • Death-associated protein kinase (DAPK) is a member of the Ca(2+)/calmodulin-regulated family of serine/threonine protein kinases. The role of the kinase activity of DAPK in eukaryotic cell apoptosis and the ability of bioavailable DAPK inhibitors to ...

    Death-associated protein kinase (DAPK) is a member of the Ca(2+)/calmodulin-regulated family of serine/threonine protein kinases. The role of the kinase activity of DAPK in eukaryotic cell apoptosis and the ability of bioavailable DAPK inhibitors to rescue neuronal death after brain injury have made it a drug-discovery target for neurodegenerative disorders. In order to understand the recognition of nucleotides by DAPK and to gain insight into DAPK catalysis, the crystal structure of human DAPK was solved in complex with ADP and Mg(2+) at 1.85 A resolution. ADP is a product of the kinase reaction and product release is considered to be the rate-limiting step of protein kinase catalytic cycles. The structure of DAPK-ADP-Mg(2+) was compared with a newly determined DAPK-AMP-PNP-Mg(2+) structure and the previously determined apo DAPK structure (PDB code 1jks). The comparison shows that nucleotide-induced changes are localized to the glycine-rich loop region of DAPK.

    Organizational Affiliation: 

    Center for Drug Discovery and Chemical Biology, Northwestern University, Chicago, Illinois 60611, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Death-associated protein kinase 1A294Homo sapiensMutation(s): 0 
Gene Names: DAPK1, DAPK
EC: 2.7.11.1
Find proteins for P53355 (Homo sapiens)
Explore P53355 
Go to UniProtKB:  P53355
NIH Common Fund Data Resources
PHAROS  P53355
GTEx  ENSG00000196730
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.862α = 90
b = 62.675β = 90
c = 88.23γ = 90
Software Package:
Software NamePurpose
BLU-MAXdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance