4QFS

Structure of AMPK in complex with Br2-A769662core activator and STAUROSPORINE inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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
  • Structures With Same Primary Citation

  • 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. Electronic address: ravi.g.kurumbail@pfizer.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-1A503Rattus norvegicusMutation(s): 0 
Gene Names: Ampk1Prkaa1
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)
Find proteins for P54645 (Rattus norvegicus)
Explore P54645 
Go to UniProtKB:  P54645
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-1B204Rattus norvegicusMutation(s): 1 
Gene Names: Prkab1
Find proteins for P80386 (Rattus norvegicus)
Explore P80386 
Go to UniProtKB:  P80386
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit gamma-1C330Rattus norvegicusMutation(s): 0 
Gene Names: Prkag1
Find proteins for P80385 (Rattus norvegicus)
Explore P80385 
Go to UniProtKB:  P80385
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STU
Query on STU

Download CCD File 
A
STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
32H
Query on 32H

Download CCD File 
A
2-bromo-3-(4-bromophenyl)-4-hydroxy-6-oxo-6,7-dihydrothieno[2,3-b]pyridine-5-carbonitrile
C14 H6 Br2 N2 O2 S
BLJQBTCHXOTSEZ-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download CCD File 
C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.88α = 90
b = 123.88β = 90
c = 401.64γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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