1OCN

Mutant D416A of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with a cellobio-derived isofagomine at 1.3 angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

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This is version 1.3 of the entry. See complete history. 


Literature

Distortion of a Cellobio-Derived Isofagomine Highlights the Potential Conformational Itinerary of Inverting Beta-Glucosidases

Varrot, A., Macdonald, J., Stick, R.V., Pell, G., Gilbert, H.J., Davies, G.J.

(2003) Chem Commun (Camb) 21: 946

  • DOI: https://doi.org/10.1039/b301592k
  • Primary Citation of Related Structures:  
    1OCN

  • PubMed Abstract: 

    A cellobio-derived isofagomine glycosidase inhibitor (Ki approximately 400 nM) displays an unusual distorted 2,5B (boat) conformation upon binding to cellobiohydrolase Cel6A from Humicola insolens, highlighting the different conformational itineraries used by various glycosidases, with consequences for the design of therapeutic agents.

    • Organizational Affiliation: 

    Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, UK Y010 5YW.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CELLOBIOHYDROLASE II362Humicola insolensMutation(s): 0 
EC: 3.2.1.91
UniProt
Find proteins for Q9C1S9 (Humicola insolens)
Explore Q9C1S9 
Go to UniProtKB:  Q9C1S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C1S9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BGC
Query on BGC
Download Ideal Coordinates CCD File 
D [auth A],
F [auth A]		beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
IFM
Query on IFM
Download Ideal Coordinates CCD File 
C [auth A],
E [auth A]		5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.357α = 90
b = 69.842β = 113.52
c = 51.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-22
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary