Agonist bound human A2a adenosine receptor with D52N mutation at 2.60 A resolution

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 

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Structural Connection between Activation Microswitch and Allosteric Sodium Site in GPCR Signaling.

White, K.L.Eddy, M.T.Gao, Z.G.Han, G.W.Lian, T.Deary, A.Patel, N.Jacobson, K.A.Katritch, V.Stevens, R.C.

(2018) Structure 26: 259-269.e5

  • DOI: https://doi.org/10.1016/j.str.2017.12.013
  • Primary Citation of Related Structures:  
    5WF5, 5WF6

  • PubMed Abstract: 

    Sodium ions are endogenous allosteric modulators of many G-protein-coupled receptors (GPCRs). Mutation of key residues in the sodium binding motif causes a striking effect on G-protein signaling. We report the crystal structures of agonist complexes for two variants in the first sodium coordination shell of the human A 2A adenosine receptor, D52 2.50 N and S91 3.39 A. Both structures present an overall active-like conformation; however, the variants show key changes in the activation motif NPxxY. Changes in the hydrogen bonding network in this microswitch suggest a possible mechanism for modified G-protein signaling and enhanced thermal stability. These structures, signaling data, and thermal stability analysis with a panel of pharmacological ligands provide a basis for understanding the role of the sodium-coordinating residues on stability and G-protein signaling. Utilizing the D 2.50 N variant is a promising method for stabilizing class A GPCRs to accelerate structural efforts and drug discovery.

  • Organizational Affiliation

    Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Human A2a adenosine receptor T4L chimera504Homo sapiensTequatrovirus T4Mutation(s): 5 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
OLC (Subject of Investigation/LOI)
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
Binding Affinity Annotations 
IDSourceBinding Affinity
UKA BindingDB:  5WF5 Ki: 4 (nM) from 1 assay(s)
IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.686α = 90
b = 77.769β = 101.05
c = 86.488γ = 90
Software Package:
Software NamePurpose
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: 2018-02-21
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description