3RX7

Structure of AaCel9A in complex with cellotetraose-like isofagomine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history. 


Literature

Fortuitious binding of inhibitors-derived isofagomine for inverting GH9 beta-glycosidases

Morera, S., Vigouroux, A., Stubbs, K.A.

(2011) Org Biomol Chem 9: 5945-5947

  • DOI: https://doi.org/10.1039/c1ob05766a
  • Primary Citation of Related Structures:  
    3RX5, 3RX7, 3RX8

  • PubMed Abstract: 

    Using structural insight, the binding mode of isofagomine-derived inhibitors with family GH9 glycosidases is achieved via the study of Alicyclobacillus acidocaldarius (AaCel9A) endoglucanase. In contrast to what was observed in the first report using these compounds with inverting glycosidases from family GH6, these inhibitors do not adopt a distorted conformation in the active site.

    • Organizational Affiliation: 

    Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France. [email protected]


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellulase537Alicyclobacillus acidocaldarius subsp. acidocaldariusMutation(s): 0 
Gene Names: celA
EC: 3.2.1.4
UniProt
Find proteins for Q9AJS0 (Alicyclobacillus acidocaldarius subsp. acidocaldarius)
Explore Q9AJS0 
Go to UniProtKB:  Q9AJS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AJS0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G3I
Query on G3I
Download Ideal Coordinates CCD File 
D [auth A](3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranosyl-(1->4)-beta-D-glucopyranoside
C24 H43 N O18
WWLNURYAWFMUKB-QPKZCLDCSA-N
9MR
Query on 9MR
Download Ideal Coordinates CCD File 
E [auth A](3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside
C12 H23 N O8
LEOSSOWHBSKZSO-WUYFHPBOSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G3I PDBBind:  3RX7 Ki: 940 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.22α = 90
b = 129.09β = 90
c = 49.19γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2011-08-24 
    • Deposition Author(s): Morera, S.

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary