The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManMIm

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

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This is version 1.1 of the entry. See complete history


Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate.

Williams, R.J.Iglesias-Fernandez, J.Stepper, J.Jackson, A.Thompson, A.J.Lowe, E.C.White, J.M.Gilbert, H.J.Rovira, C.Davies, G.J.Williams, S.J.

(2014) Angew Chem Int Ed Engl 53: 1087

  • DOI: https://doi.org/10.1002/anie.201308334
  • Primary Citation of Related Structures:  
    4CD4, 4CD5, 4CD6, 4CD7, 4CD8

  • PubMed Abstract: 

    Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including β-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition.

  • Organizational Affiliation

    School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic 3010 (Australia).

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDO-BETA-1,4-MANNANASE320Alicyclobacillus acidocaldariusMutation(s): 0 
Find proteins for A5H1I6 (Alicyclobacillus acidocaldarius)
Explore A5H1I6 
Go to UniProtKB:  A5H1I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5H1I6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MVL

Download Ideal Coordinates CCD File 
C8 H12 N2 O4
Query on BMA

Download Ideal Coordinates CCD File 
C [auth A]beta-D-mannopyranose
C6 H12 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.47 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.82α = 90
b = 75.89β = 90
c = 91.48γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary