4AYP

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with thiomannobioside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.097 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach.

Thompson, A.J.Dabin, J.Iglesias-Fernandez, J.Ardevol, A.Dinev, Z.Williams, S.J.Bande, O.Siriwardena, A.Moreland, C.Hu, T.C.Smith, D.K.Gilbert, H.J.Rovira, C.Davies, G.J.

(2012) Angew Chem Int Ed Engl 51: 10997

  • DOI: https://doi.org/10.1002/anie.201205338
  • Primary Citation of Related Structures:  
    4AYO, 4AYP, 4AYQ, 4AYR

  • PubMed Abstract: 

    Mannosides in the southern hemisphere: Conformational analysis of enzymatic mannoside hydrolysis informs strategies for enzyme inhibition and inspires solutions to mannoside synthesis. Atomic resolution structures along the reaction coordinate of an inverting α-mannosidase show how the enzyme distorts the substrate and transition state. QM/MM calculations reveal how the free energy landscape of isolated α-D-mannose is molded on enzyme to only allow one conformationally accessible reaction coordinate.


  • Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.


Macromolecules
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 
EC: 3.2.1.113
UniProt
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside
B
2N/AN/A
Glycosylation Resources
GlyTouCan:  G32183TR
GlyCosmos:  G32183TR
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.097 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.135α = 90
b = 144.135β = 90
c = 50.301γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary