3QAK

Agonist bound structure of the human adenosine A2a receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UKAClick on this verticalbar to view detailsBest fitted OLCClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

Structure of an agonist-bound human A2A adenosine receptor.

Xu, F.Wu, H.Katritch, V.Han, G.W.Jacobson, K.A.Gao, Z.G.Cherezov, V.Stevens, R.C.

(2011) Science 332: 322-327

  • DOI: https://doi.org/10.1126/science.1202793
  • Primary Citation of Related Structures:  
    3QAK

  • PubMed Abstract: 

    Activation of G protein-coupled receptors upon agonist binding is a critical step in the signaling cascade for this family of cell surface proteins. We report the crystal structure of the A(2A) adenosine receptor (A(2A)AR) bound to an agonist UK-432097 at 2.7 angstrom resolution. Relative to inactive, antagonist-bound A(2A)AR, the agonist-bound structure displays an outward tilt and rotation of the cytoplasmic half of helix VI, a movement of helix V, and an axial shift of helix III, resembling the changes associated with the active-state opsin structure. Additionally, a seesaw movement of helix VII and a shift of extracellular loop 3 are likely specific to A(2A)AR and its ligand. The results define the molecule UK-432097 as a "conformationally selective agonist" capable of receptor stabilization in a specific active-state configuration.


  • Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine receptor A2a,lysozyme chimera488Homo sapiensTequatrovirus T4Mutation(s): 2 
Gene Names: ADORA2ADORA2AE
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P29274
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UKA
Query on UKA

Download Ideal Coordinates CCD File 
B [auth A]6-(2,2-diphenylethylamino)-9-[(2R,3R,4S,5S)-5-(ethylcarbamoyl)-3,4-dihydroxy-oxolan-2-yl]-N-[2-[(1-pyridin-2-ylpiperidin-4-yl)carbamoylamino]ethyl]purine-2-carboxamide
C40 H47 N11 O6
ZOTHAEBAWXWVID-HXEFRTELSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UKA BindingDB:  3QAK Ki: 4 (nM) from 1 assay(s)
IC50: 4 (nM) from 1 assay(s)
PDBBind:  Ki: 4.75 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.836α = 90
b = 78.944β = 100.54
c = 86.579γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UKAClick on this verticalbar to view detailsBest fitted OLCClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Structure summary
  • Version 1.3: 2012-10-10
    Changes: Database references
  • Version 1.4: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.5: 2018-01-24
    Changes: Structure summary
  • Version 1.6: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary