2XIB

CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH DEOXYFUCONOJIRIMYCIN

PDB DOI: https://doi.org/10.2210/pdb2XIB/pdb

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

Deposited: 2010-06-28 Released: 2010-07-21
Deposition Author(s): Lammerts van Bueren, A., Popat, S.D., Lin, C.H., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.235
R-Value Work: 0.185
R-Value Observed: 0.188

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 211.29 kDa
Atom Count: 15,070
Modelled Residue Count: 1,748
Deposited Residue Count: 1,812
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	A, B, C, D	453	Bacteroides thetaiotaomicron	Mutation(s): 0
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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A3I4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DFU Query on DFU Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	E [auth A], I [auth B], M [auth C], P [auth D]	(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL C₆ H₁₃ N O₃ VYOCYWDJTQRZLC-KCDKBNATSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain P [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	F [auth A], G [auth A], J [auth B], N [auth C], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	H [auth A], K [auth B], L [auth B], O [auth C], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
DFU	PDBBind: 2XIB	Kd: 55.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.235
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.68	α = 90
b = 185.99	β = 94.75
c = 97.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

View Full Validation Report

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 (Full details and data files)

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