2OOY

Crystal structure of the adenylate sensor from AMP-activated protein kinase complexed with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.195 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase.

Townley, R.Shapiro, L.

(2007) Science 315: 1726-1729

  • DOI: 10.1126/science.1137503
  • Primary Citation of Related Structures:  
    2OOX, 2OOY

  • PubMed Abstract: 
  • The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2 ...

    The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SNF1-like protein kinase ssp2A,
D [auth C]
137Schizosaccharomyces pombeMutation(s): 0 
Gene Names: ssp2SPCC74.03c
EC: 2.7.11.1
UniProt
Find proteins for O74536 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Go to UniProtKB:  O74536
Entity Groups  
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UniProt GroupO74536
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SPCC1919.03c proteinB,
E [auth D]
97Schizosaccharomyces pombeMutation(s): 0 
Gene Names: SPCC1919.03c
UniProt
Find proteins for P78789 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Go to UniProtKB:  P78789
Entity Groups  
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UniProt GroupP78789
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical protein C1556.08c in chromosome IF [auth E],
C [auth G]
333Schizosaccharomyces pombeMutation(s): 0 
Gene Names: SPAC1556.08cSPAC1F12.01c
UniProt
Find proteins for Q10343 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q10343 
Go to UniProtKB:  Q10343
Entity Groups  
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UniProt GroupQ10343
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
G,
I [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
H [auth E]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.902α = 90
b = 77.666β = 123.99
c = 107.576γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance