1OCQ

COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION with cellobio-derived isofagomine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Direct Observation of the Protonation State of an Imino Sugar Glycosidase Inhibitor Upon Binding

Varrot, A.Tarling, C.A.Macdonald, J.M.Stick, R.V.Zechel, D.L.Withers, S.G.Davies, G.J.

(2003) J Am Chem Soc 125: 7496

  • DOI: https://doi.org/10.1021/ja034917k
  • Primary Citation of Related Structures:  
    1OCQ

  • PubMed Abstract: 

    Glycosidases are some of the most ubiquitous enzyme in nature. Their biological significance, coupled to their enormous catalytic prowess derived from tight binding of the transition state, is reflected in their importance as therapeutic targets. Many glycosidase inhibitors are known. Imino sugars are often potent inhibitors, yet many facets of their mode of action, such as their degree, if any, of transition-state "mimicry" and their protonation state when bound to the target glycosidase remain unclear. Atomic resolution analysis of the endoglucanase, Cel5A, in complex with a cellobio-derived isofagomine in conjunction with the pH dependence of Ki and kcat/KM reveals that this compound binds as a protonated sugar. Surprisingly, both the enzymatic nucleophile and the acid/base are unprotonated in the complex.


  • Organizational Affiliation

    Department of Chemistry, Structural Biology Laboratory, The University of York, Heslington, York YO10 5YW, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDOGLUCANASE 5A303Salipaludibacillus agaradhaerensMutation(s): 0 
EC: 3.2.1.4
UniProt
Find proteins for O85465 (Salipaludibacillus agaradhaerens)
Explore O85465 
Go to UniProtKB:  O85465
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO85465
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.115 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.023α = 90
b = 69.677β = 90
c = 76.899γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-26
    Type: Initial release
  • Version 1.1: 2015-07-22
    Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance
  • Version 1.2: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary