1JKK

2.4A X-RAY STRUCTURE OF TERNARY COMPLEX OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE WITH ATP ANALOGUE AND MG.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression.

Tereshko, V., Teplova, M., Brunzelle, J., Watterson, D.M., Egli, M.

(2001) Nat Struct Biol 8: 899-907

  • DOI: 10.1038/nsb1001-899
  • Primary Citation of Related Structures:  
    1IG1, 1JKL, 1JKK, 1JKT, 1JKS

  • PubMed Abstract: 

    • We have determined X-ray crystal structures with up to 1.5 A resolution of the catalytic domain of death-associated protein kinase (DAPK), the first described member of a novel family of pro-apoptotic and tumor-suppressive serine/threonine kinases. T ...

    We have determined X-ray crystal structures with up to 1.5 A resolution of the catalytic domain of death-associated protein kinase (DAPK), the first described member of a novel family of pro-apoptotic and tumor-suppressive serine/threonine kinases. The geometry of the active site was studied in the apo form, in a complex with nonhydrolyzable AMPPnP and in a ternary complex consisting of kinase, AMPPnP and either Mg2+ or Mn2+. The structures revealed a previously undescribed water-mediated stabilization of the interaction between the lysine that is conserved in protein kinases and the beta- and gamma-phosphates of ATP, as well as conformational changes at the active site upon ion binding. Comparison between these structures and nucleotide triphosphate complexes of several other kinases disclosed a number of unique features of the DAPK catalytic domain, among which is a highly ordered basic loop in the N-terminal domain that may participate in enzyme regulation.

    Organizational Affiliation: 

    Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEATH-ASSOCIATED PROTEIN KINASEA294Homo sapiensMutation(s): 0 
Gene Names: DAPK1, DAPK
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
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
ANP
Query on ANP
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.63α = 90
b = 62.43β = 90
c = 88.67γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance