Crystal structure of death associated protein kinase in complex with ADP and Mg2+

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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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: https://doi.org/10.1107/S0907444908043679
  • Primary Citation of Related Structures:  
    3EH9, 3EHA, 3F5G, 3F5U

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Death-associated protein kinase 1294Homo sapiensMutation(s): 0 
Gene Names: DAPKDAPK1death-associated protein kinase 1
UniProt & NIH Common Fund Data Resources
Find proteins for P53355 (Homo sapiens)
Explore P53355 
Go to UniProtKB:  P53355
GTEx:  ENSG00000196730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53355
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C10 H15 N5 O10 P2
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.807α = 90
b = 62.545β = 90
c = 88.396γ = 90
Software Package:
Software NamePurpose
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description