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 

wwPDB Validation 3D Report Full Report


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:  

  • 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 enz ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-1
A
503Rattus norvegicusMutation(s): 0 
Gene Names: Prkaa1 (Ampk1)
EC: 2.7.11.1
Find proteins for P54645 (Rattus norvegicus)
Go to UniProtKB:  P54645
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-1
B
204Rattus norvegicusMutation(s): 1 
Gene Names: Prkab1
Find proteins for P80386 (Rattus norvegicus)
Go to UniProtKB:  P80386
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit gamma-1
C
330Rattus norvegicusMutation(s): 0 
Gene Names: Prkag1
Find proteins for P80385 (Rattus norvegicus)
Go to UniProtKB:  P80385
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
STU
Query on STU

Download SDF File 
Download CCD File 
A
STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
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 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 124.370α = 90.00
b = 124.370β = 90.00
c = 404.060γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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