Crystal structure of the Propionibacterium acnes surface sialidase in complex with Neu5Ac2en

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Crystal structure of the Propionibacterium acnes surface sialidase, a drug target for P. acnes-associated diseases.

Yu, A.C.Y.Volkers, G.Jongkees, S.A.K.Worrall, L.J.Withers, S.G.Strynadka, N.C.J.

(2022) Glycobiology 32: 162-170

  • DOI: https://doi.org/10.1093/glycob/cwab094
  • Primary Citation of Related Structures:  
    7LBU, 7LBV

  • PubMed Abstract: 

    Propionibacterium acnes, though generally considered part of the normal flora of human skin, is an opportunistic pathogen associated with acne vulgaris as well as other diseases, including endocarditis, endophthalmitis and prosthetic joint infections. Its virulence potential is also supported by knowledge gained from its sequenced genome. Indeed, a vaccine targeting a putative cell wall-anchored P. acnes sialidase has been shown to suppress cytotoxicity and pro-inflammatory cytokine release induced by the organism, and is proposed as an alternative treatment for P. acnes-associated diseases. Here, we report the crystal structures of the surface sialidase and its complex with the transition-state mimic Neu5Ac2en. Our structural and kinetic analyses, together with insight from a glycan array screen, which probes subtle specificities of the sialidase for α-2,3-sialosides, provide a basis for the structure-based design of novel small-molecule therapeutics against P. acnes infections.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exo-alpha-sialidase455Cutibacterium acnesMutation(s): 0 
Gene Names: B1B09_09755FD518_10685
Find proteins for A0A8B2VIR8 (Cutibacterium acnes)
Explore A0A8B2VIR8 
Go to UniProtKB:  A0A8B2VIR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8B2VIR8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAN (Subject of Investigation/LOI)
Query on DAN

Download Ideal Coordinates CCD File 
C11 H17 N O8
Query on PO4

Download Ideal Coordinates CCD File 
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.978α = 116.93
b = 46.65β = 99.1
c = 49.659γ = 91.73
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description