1JKK | pdb_00001jkk

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:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.40 Å
  • R-Value Free:&nbsp
    0.239 (Depositor), 0.250 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.204 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.204&nbsp(Depositor)&nbsp

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Literature

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

Tereshko, V.,&nbspTeplova, M.,&nbspBrunzelle, J.,&nbspWatterson, D.M.,&nbspEgli, M.

(2001) Nat Struct Biol&nbsp8: 899-907

  • DOI:&nbsphttps://doi.org/10.1038/nsb1001-899
  • Primary Citation of Related Structures: &nbsp
    1IG1, 1JKK, 1JKL, 1JKS, 1JKT

  • PubMed Abstract:&nbsp

    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:&nbsp

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEATH-ASSOCIATED PROTEIN KINASE294Homo sapiensMutation(s): 0&nbsp
EC:&nbsp2.7.1&nbsp(PDB Primary Data),&nbsp2.7.11.1&nbsp(UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP53355&nbsp(Homo sapiens)
Explore&nbspP53355&nbsp
Go to UniProtKB: &nbspP53355
PHAROS: &nbspP53355
GTEx: &nbspENSG00000196730&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53355
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.40 Å
  • R-Value Free:&nbsp 0.239 (Depositor), 0.250 (DCC)&nbsp
  • R-Value Work:&nbsp 0.204 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Observed:&nbsp0.204&nbsp(Depositor)&nbsp
Space Group:&nbspP 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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Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations