ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribose

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


(ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition.

Rack, J.G.M.Ariza, A.Drown, B.S.Henfrey, C.Bartlett, E.Shirai, T.Hergenrother, P.J.Ahel, I.

(2018) Cell Chem Biol 25: 1533-1546.e12

  • DOI: https://doi.org/10.1016/j.chembiol.2018.11.001
  • Primary Citation of Related Structures:  
    6G1P, 6G1Q, 6G28, 6G2A, 6HGZ, 6HH3, 6HH4, 6HH5, 6HH6, 6HOZ

  • PubMed Abstract: 

    Protein ADP-ribosylation is a highly dynamic post-translational modification. The rapid turnover is achieved, among others, by ADP-(ribosyl)hydrolases (ARHs), an ancient family of enzymes that reverses this modification. Recently ARHs came into focus due to their role as regulators of cellular stresses and tumor suppressors. Here we present a comprehensive structural analysis of the enzymatically active family members ARH1 and ARH3. These two enzymes have very distinct substrate requirements. Our data show that binding of the adenosine ribose moiety is highly diverged between the two enzymes, whereas the active sites harboring the distal ribose closely resemble each other. Despite this apparent similarity, we elucidate the structural basis for the selective inhibition of ARH3 by the ADP-ribose analogues ADP-HPD and arginine-ADP-ribose. Together, our biochemical and structural work provides important insights into the mode of enzyme-ligand interaction, helps to understand differences in their catalytic behavior, and provides useful tools for targeted drug design.

  • Organizational Affiliation

    Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylhydrolase like 2
A, B
350Latimeria chalumnaeMutation(s): 0 
Gene Names: ADPRHL2
Find proteins for H3BCW1 (Latimeria chalumnae)
Explore H3BCW1 
Go to UniProtKB:  H3BCW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH3BCW1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AR6

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C15 H23 N5 O14 P2
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.905α = 90
b = 97.458β = 90
c = 105.503γ = 90
Software Package:
Software NamePurpose
xia2data reduction
DIALSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2018-11-28 
  • Deposition Author(s): Ariza, A.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101794

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-02
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary