RCSB PDB - 1ATP: 2.2 angstrom refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MNATP and a peptide inhibitor

 1ATP

2.2 angstrom refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MNATP and a peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.177 

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Ligand Structure Quality Assessment 

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This is version 1.5 of the entry. See complete history


Literature

2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor.

Zheng, J.Trafny, E.A.Knighton, D.R.Xuong, N.H.Taylor, S.S.Ten Eyck, L.F.Sowadski, J.M.

(1993) Acta Crystallogr D Biol Crystallogr 49: 362-365

  • DOI: https://doi.org/10.1107/S0907444993000423
  • Primary Citation of Related Structures:  
    1ATP

  • PubMed Abstract: 

    . The crystal structure of a ternary complex containing the catalytic subunit of cAMP-dependent protein kinase, ATP and a 20-residue inhibitor peptide was refined at a resolution of 2.2 A to an R value of 0.177. In order to identify the metal binding sites, the crystals, originally grown in the presence of low concentrations of Mg(2+), were soaked in Mn(2+). Two Mn(2+) ions were identified using an anomalous Fourier map. One Mn(2+) ion bridges the gamma- and beta-phosphates and interacts with Asp184 and two water molecules. The second Mn(2+) ion interacts with the side chains of Asn171 and Asp l84 as well as with a water molecule. Modeling a serine into the P site of the inhibitor peptide suggests a mechanism for phosphotransfer.


  • Organizational Affiliation

    Department of Chemistry, University of California, San Diego, La Jolla 92093-0654, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-DEPENDENT PROTEIN KINASEA [auth E]350Mus musculusMutation(s): 0 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt
Find proteins for P05132 (Mus musculus)
Explore P05132 
Go to UniProtKB:  P05132
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05132
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDE INHIBITOR PKI(5-24)B [auth I]20Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63248 (Mus musculus)
Explore P63248 
Go to UniProtKB:  P63248
IMPC:  MGI:104747
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63248
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A [auth E]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A [auth E]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.58α = 90
b = 76.28β = 90
c = 80.58γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ATPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary