Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.32 kDa 
• Atom Count: 2404 
• Modelled Residue Count: 277 
• Deposited Residue Count: 294 
• Unique protein chains: 1

1JKK

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

• DOI: 10.2210/pdb1JKK/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-07-12 Released: 2002-04-01 
• Deposition Author(s): Tereshko, V., Teplova, M., Brunzelle, J., Watterson, D.M., Egli, M.

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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 

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

• PubMed: 11573098 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEATH-ASSOCIATED PROTEIN KINASE	A	294	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 46.63	α = 90
b = 62.43	β = 90
c = 88.67	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-12 
• Released Date: 2002-04-01 
Deposition Author(s): Tereshko, V., Teplova, M., Brunzelle, J., Watterson, D.M., Egli, M.

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