2ZXB

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

PDB DOI: https://doi.org/10.2210/pdb2ZXB/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.244
R-Value Work: 0.172
R-Value Observed: 0.176

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 106.65 kDa
Atom Count: 7,668
Modelled Residue Count: 884
Deposited Residue Count: 910
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WYE2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZXB Query on ZXB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	(2S,3R,4S,5R)-2-benzylpiperidine-3,4,5-triol C₁₂ H₁₇ N O₃ NDQBRGWFAQLRFZ-QCNOEVLYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
ZXB	PDBBind: 2ZXB	Ki: 5000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.244
R-Value Work: 0.172
R-Value Observed: 0.176
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.517	α = 90
b = 179.517	β = 90
c = 169.098	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary