Crystal structure of family 47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with kifunensine

Experimental Data Snapshot

  • Resolution: 1.05 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach.

Males, A.Raich, L.Williams, S.J.Rovira, C.Davies, G.J.

(2017) Chembiochem 18: 1496-1501

  • DOI: https://doi.org/10.1002/cbic.201700166
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The varied yet family-specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly binding and specific enzyme inhibitors. A cardinal example of a GH-family-specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is a low-nanomolar inhibitor that is selective for GH family 47 inverting α-mannosidases. Here we show, through quantum-mechanical approaches, that kifunensine is restrained to a "ring-flipped" 1 C 4 conformation with another accessible, but higher-energy, region around the 1,4 B conformation. The conformations of kifunensine in complex with a range of GH47 enzymes-including an atomic-level resolution (1 Å) structure of kifunensine with Caulobacter sp. CkGH47 reported herein and with GH family 38 and 92 α-mannosidases-were mapped onto the kifunensine free-energy landscape. These studies revealed that kifunensine has the ability to mimic the product state of GH47 enzymes but cannot mimic any conformational states relevant to the reaction coordinate of mannosidases from other families.

  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, The University of York, York, YO10 5DD, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannosyl-oligosaccharide 1,2-alpha-mannosidase447Caulobacter sp. K31Mutation(s): 0 
Gene Names: Caul_4035
Find proteins for B0SWV2 (Caulobacter sp. (strain K31))
Explore B0SWV2 
Go to UniProtKB:  B0SWV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0SWV2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.05 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.146 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.923α = 90
b = 144.923β = 90
c = 50.593γ = 120
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Author supporting evidence
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations