2ZXD | pdb_00002zxd

alpha-L-fucosidase complexed with inhibitor, iso-6FNJ

• PDB DOI: https://doi.org/10.2210/pdb2ZXD/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-22 Released: 2009-12-08 
• Deposition Author(s): Wu, H.-J., Ko, T.-P., Ho, C.-W., Lin, C.-H., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Structural basis of alpha-fucosidase inhibition by iminocyclitols with K(i) values in the micro- to picomolar range.

Wu, H.J., Ho, C.W., Ko, T.P., Popat, S.D., Lin, C.H., Wang, A.H.

(2010) Angew Chem Int Ed Engl 49: 337-340

• PubMed: 19967696 
• DOI: https://doi.org/10.1002/anie.200905597
• Primary Citation Related Structures: 
  2ZWZ, 2ZX5, 2ZX6, 2ZX7, 2ZX8, 2ZX9, 2ZXA, 2ZXB, 2ZXD

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Organizational Affiliation: 
• Institute of Biological Chemistry, CBMB, Taiwan International Graduate Program, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 11529, Taiwan.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 106.55 kDa 
• Atom Count: 7,857 
• Modeled Residue Count: 882 
• Deposited Residue Count: 910 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-fucosidase, putative	A, B	455	Thermotoga maritima	Mutation(s): 0  EC: 3.2.1.51
UniProt
Find proteins for Q9WYE2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYE2  Go to UniProtKB:  Q9WYE2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZXD	C [auth A], D [auth B]	(2S,3R,4S,5R)-2-(1-methylethyl)piperidine-3,4,5-triol C8 H17 N O3 WNBLNSHOIGFFFW-VGRMVHKJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.012	α = 90
b = 181.012	β = 90
c = 170.322	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Wu, H.-J., Ko, T.-P., Ho, C.-W., Lin, C.-H., Wang, A.H.-J.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary