2XII

CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH AN EXTENDED 9-FLUORENONE IMINOSUGAR INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb2XII/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-30 Released: 2010-07-21 
• Deposition Author(s): Lammerts van Bueren, A., Popat, S.D., Lin, C.H., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Structural and Thermodynamic Analyses of Alpha-L-Fucosidase Inhibitors.

Lammerts Van Bueren, A., Popat, S.D., Lin, C.H., Davies, G.J.

(2010) Chembiochem 11: 1971

• PubMed: 20665773 
• DOI: https://doi.org/10.1002/cbic.201000339
• Primary Citation of Related Structures:  
  2XIB, 2XII

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Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 106.42 kDa 
• Atom Count: 7,973 
• Modelled Residue Count: 877 
• Deposited Residue Count: 906 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-L-FUCOSIDASE	A, B	453	Bacteroides thetaiotaomicron	Mutation(s): 0  EC: 3.2.1.51
UniProt
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3I4  Go to UniProtKB:  Q8A3I4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TA9	D [auth A], I [auth B]	9-oxo-N-[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyl-piperidin-2-yl]methyl]fluorene-1-carboxamide C21 H22 N2 O5 NQPIYVRYYGVNCF-KOOFZGQNSA-N
TYR	C [auth A], H [auth B]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
SO4	E [auth A], F [auth A], G [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TA9	Binding MOAD:  2XII	Kd: 63.3 (nM) from 1 assay(s)
	PDBBind:  2XII	Kd: 63.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.466	α = 90
b = 85.08	β = 108.52
c = 120.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Lammerts van Bueren, A., Popat, S.D., Lin, C.H., Davies, G.J.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description