Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34324.87 
• Atom Count: 2277 
• 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


• 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: 2.4 Å
• R-Value Free: 0.239 
• R-Value Work: 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.Mol.Biol. 8: 899-907

• PubMed: 11573098 
• DOI: 10.1038/nsb1001-899
• Primary Citation of Related Structures:  
  1JKT, 1JKS, 1JKL, 1IG1


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DEATH-ASSOCIATED PROTEIN KINASE	A	294	Homo sapiens	Mutation(s): 0  Gene Names: DAPK1 (DAPK) EC: 2.7.11.1
Find proteins for P53355 (Homo sapiens) Go to Gene View: DAPK1 Go to UniProtKB:  P53355

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.239 
• R-Value Work: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 46.630	α = 90.00
b = 62.430	β = 90.00
c = 88.670	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
CNS	refinement
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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance