3QAK | pdb_00003qak

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 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 56.23 kDa 
  • Atom Count: 3,568 
  • Modeled Residue Count: 444 
  • Deposited Residue Count: 488 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
GTEx:  ENSG00000128271 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P29274
Sequence Annotations
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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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
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 


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