XFEL beta2 AR structure by ligand exchange from Alprenolol to Timolol.

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Toward G protein-coupled receptor structure-based drug design using X-ray lasers.

Ishchenko, A.Stauch, B.Han, G.W.Batyuk, A.Shiriaeva, A.Li, C.Zatsepin, N.Weierstall, U.Liu, W.Nango, E.Nakane, T.Tanaka, R.Tono, K.Joti, Y.Iwata, S.Moraes, I.Gati, C.Cherezov, V.

(2019) IUCrJ 6: 1106-1119

  • DOI: https://doi.org/10.1107/S2052252519013137
  • Primary Citation of Related Structures:  
    6PRZ, 6PS0, 6PS1, 6PS2, 6PS3, 6PS4, 6PS5, 6PS6, 6PS7, 6PS8

  • PubMed Abstract: 

    Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β 2 -adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.

  • Organizational Affiliation

    Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of Beta-2 adrenergic receptor and T4 lysozyme506Homo sapiensTequatrovirus T4Mutation(s): 6 
Gene Names: ADRB2ADRB2RB2AReT4Tp126
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P07550 (Homo sapiens)
Explore P07550 
Go to UniProtKB:  P07550
PHAROS:  P07550
GTEx:  ENSG00000169252 
Find proteins for D9IEF7 (Enterobacteria phage T4)
Explore D9IEF7 
Go to UniProtKB:  D9IEF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsD9IEF7P07550
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CLR

Download Ideal Coordinates CCD File 
C27 H46 O
Query on OLC

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G [auth A],
H [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
TIM (Subject of Investigation/LOI)
Query on TIM

Download Ideal Coordinates CCD File 
B [auth A](2S)-1-(tert-butylamino)-3-[(4-morpholin-4-yl-1,2,5-thiadiazol-3-yl)oxy]propan-2-ol
C13 H24 N4 O3 S
Query on OLA

Download Ideal Coordinates CCD File 
C18 H34 O2
Query on SO4

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C [auth A],
D [auth A],
E [auth A]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.73α = 90
b = 76.33β = 90
c = 172γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127086

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description