3RX8

structure of AaCel9A in complex with cellobiose-like isofagomine

• PDB DOI: https://doi.org/10.2210/pdb3RX8/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-10 Released: 2011-08-24 
• Deposition Author(s): Morera, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.234 
• R-Value Work: 0.164 
• R-Value Observed: 0.168 

Starting Model: experimental

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

• PubMed: 21785782 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.87 kDa 
• Atom Count: 4,208 
• Modelled Residue Count: 528 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulase	A	537	Alicyclobacillus acidocaldarius subsp. acidocaldarius	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9MR	E [auth A], F [auth A]	(3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl beta-D-glucopyranoside C12 H23 N O8 LEOSSOWHBSKZSO-WUYFHPBOSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9MR	PDBBind:  3RX8	Ki: 610 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 0.234 
• R-Value Work: 0.164 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.41	α = 90
b = 129.34	β = 90
c = 49.39	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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