3AGM

Complex of PKA with the bisubstrate protein kinase inhibitor ARC-670


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Diversity of bisubstrate binding modes of adenosine analogue-oligoarginine conjugates in protein kinase a and implications for protein substrate interactions.

Pflug, A.Rogozina, J.Lavogina, D.Enkvist, E.Uri, A.Engh, R.A.Bossemeyer, D.

(2010) J Mol Biol 403: 66-77

  • DOI: 10.1016/j.jmb.2010.08.028
  • Primary Citation of Related Structures:  
    3AGL, 3AGM, 3AG9

  • PubMed Abstract: 
  • Crystal structures of the catalytic subunit α of cAMP-dependent protein kinase (PKAc) with three adenosine analogue-oligoarginine conjugates (ARCs) are presented. The rationally designed ARCs include moieties that, in combination, target both the ATP ...

    Crystal structures of the catalytic subunit α of cAMP-dependent protein kinase (PKAc) with three adenosine analogue-oligoarginine conjugates (ARCs) are presented. The rationally designed ARCs include moieties that, in combination, target both the ATP- and the peptide-substrate-binding sites of PKAc, thereby taking advantage of high-affinity binding interactions offered by the ATP site while utilizing an additional mechanism for target specificity via binding to the peptide substrate site. The crystal structures demonstrate that, in accord with the previously reported bisubstrate character of ARCs, the inhibitors occupy both binding sites of PKAc. Further, they show new binding modes that may also apply to natural protein substrates of PKAc, which have not been revealed by previous crystallographic studies. The crystal structures described here contribute to the understanding of the substrate-binding patterns of PKAc and should also facilitate the design of inhibitors targeting PKAc and related protein kinases.


    Organizational Affiliation

    German Cancer Research Center, Group of Structural Biochemistry, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address: d.bossemeyer@dkfz-heidelberg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA351Homo sapiensMutation(s): 0 
Gene Names: PKACAPRKACA
EC: 2.7.11.11
Find proteins for P17612 (Homo sapiens)
Explore P17612 
Go to UniProtKB:  P17612
NIH Common Fund Data Resources
PHAROS  P17612
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N~2~-{8-OXO-8-[4-(9H-PURIN-6-YL)PIPERAZIN-1-YL]OCTANOYL}-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGININAMIDEB9N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A67Ki :  0.8199999928474426   nM  PDBBind
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001021
Query on PRD_001021
BINHIBITOR ARC-670Peptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.52α = 90
b = 85.52β = 90
c = 99.04γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Derived calculations
  • Version 1.3: 2012-12-12
    Changes: Other