4QFG

Structure of AMPK in complex with STAUROSPORINE inhibitor and in the absence of a synthetic activator

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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This is version 1.4 of the entry. See complete history. 


Literature

Structural Basis for AMPK Activation: Natural and Synthetic Ligands Regulate Kinase Activity from Opposite Poles by Different Molecular Mechanisms.

Calabrese, M.F., Rajamohan, F., Harris, M.S., Caspers, N.L., Magyar, R., Withka, J.M., Wang, H., Borzilleri, K.A., Sahasrabudhe, P.V., Hoth, L.R., Geoghegan, K.F., Han, S., Brown, J., Subashi, T.A., Reyes, A.R., Frisbie, R.K., Ward, J., Miller, R.A., Landro, J.A., Londregan, A.T., Carpino, P.A., Cabral, S., Smith, A.C., Conn, E.L., Cameron, K.O., Qiu, X., Kurumbail, R.G.

(2014) Structure 22: 1161-1172

  • DOI: 10.1016/j.str.2014.06.009
  • Primary Citation of Related Structures:  
    4QFG, 4QFR, 4QFS

  • PubMed Abstract: 

    • AMP-activated protein kinase (AMPK) is a principal metabolic regulator affecting growth and response to cellular stress. Comprised of catalytic and regulatory subunits, each present in multiple forms, AMPK is best described as a family of related enzymes ...

    AMP-activated protein kinase (AMPK) is a principal metabolic regulator affecting growth and response to cellular stress. Comprised of catalytic and regulatory subunits, each present in multiple forms, AMPK is best described as a family of related enzymes. In recent years, AMPK has emerged as a desirable target for modulation of numerous diseases, yet clinical therapies remain elusive. Challenges result, in part, from an incomplete understanding of the structure and function of full-length heterotrimeric complexes. In this work, we provide the full-length structure of the widely expressed α1β1γ1 isoform of mammalian AMPK, along with detailed kinetic and biophysical characterization. We characterize binding of the broadly studied synthetic activator A769662 and its analogs. Our studies follow on the heels of the recent disclosure of the α2β1γ1 structure and provide insight into the distinct molecular mechanisms of AMPK regulation by AMP and A769662.

    Organizational Affiliation: 

    Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA. Electronic address: ravi.g.kurumbail@pfizer.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-1A503Rattus norvegicusMutation(s): 0 
Gene Names: Ampk1, Prkaa1, PRKAA1 AMPK1
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt
Find proteins for P54645 (Rattus norvegicus)
Explore P54645 
Go to UniProtKB:  P54645
Entity Groups  
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UniProt GroupP54645
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit beta-1B204Rattus norvegicusMutation(s): 1 
Gene Names: Prkab1
UniProt
Find proteins for P80386 (Rattus norvegicus)
Explore P80386 
Go to UniProtKB:  P80386
Entity Groups  
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UniProt GroupP80386
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit gamma-1C330Rattus norvegicusMutation(s): 0 
Gene Names: Prkag1
UniProt
Find proteins for P80385 (Rattus norvegicus)
Explore P80385 
Go to UniProtKB:  P80385
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80385
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.37α = 90
b = 124.37β = 90
c = 404.06γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2014-08-20
    Changes: Database references
  • Version 1.3: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-22
    Changes: Refinement description