3RX5

structure of AaCel9A in complex with cellotriose-like isofagomine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A fortuitous binding of inhibitors-derived isofagomine for inverting GH9 beta-glycosidase

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. morera@lebs.cnrs-gif.fr


Macromolecules
Find similar proteins by:  (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
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G84824ZO
GlyCosmos:  G84824ZO
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G2I
Query on G2I

Download Ideal Coordinates CCD File 
E [auth A](3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl 4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside
C18 H33 N O13
ZIMIYDWQNDRGNF-IONZOCAKSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G2I PDBBind:  3RX5 Ki: 540 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_900005
Query on PRD_900005
B
beta-cellobioseOligosaccharide / Metabolism
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.21α = 90
b = 129.47β = 90
c = 49.31γ = 90
Software Package:
Software NamePurpose
JDirectordata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary