3RX5

structure of AaCel9A in complex with cellotriose-like isofagomine

PDB DOI: https://doi.org/10.2210/pdb3RX5/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., Vigouroux, A.

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
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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

PubMed: 21785782 Search on PubMed
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

Macromolecule Content

Total Structure Weight: 59.95 kDa
Atom Count: 4,340
Modelled Residue Count: 530
Deposited Residue Count: 537
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9AJS0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G2I Query on G2I Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
G2I	PDBBind: 3RX5	Ki: 540 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	B	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain B Interactions & Density Focus chain B

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 = 85.21	α = 90
b = 129.47	β = 90
c = 49.31	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Morera, S.

Vigouroux, A.

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