2CER | pdb_00002cer

Beta-glycosidase from Sulfolobus solfataricus in complex with phenethyl-substituted glucoimidazole

PDB DOI: https://doi.org/10.2210/pdb2CER/pdb

Classification: HYDROLASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2006-02-10 Released: 2006-09-27
Deposition Author(s): Gloster, T.M., Roberts, S., Moracci, M., Vasella, A., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.246 (Depositor), 0.245 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural, Kinetic, and Thermodynamic Analysis of Glucoimidazole-Derived Glycosidase Inhibitors.

Gloster, T.M., Roberts, S., Perugino, G., Rossi, M., Moracci, M., Panday, N., Terinek, M., Vasella, A., Davies, G.J.

(2006) Biochemistry 45: 11879

PubMed: 17002288 Search on PubMed
DOI: https://doi.org/10.1021/bi060973x
Primary Citation Related Structures:
2CEQ, 2CER, 2CES, 2CET

PubMed Abstract:
Inhibition of glycosidases has great potential in the quest for highly potent and specific drugs to treat diseases such as diabetes, cancer, and viral infections. One of the most effective ways of designing such compounds is by mimicking the transition state. Here we describe the structural, kinetic, and thermodynamic dissection of binding of two glucoimidazole-derived compounds, which are among the most potent glycosidase inhibitors reported to date, with two family 1 beta-glycosidases. Provocatively, while inclusion of the phenethyl moiety improves binding by a factor of 20-80-fold, this does not appear to result from better noncovalent interactions with the enzyme; instead, improved affinity may be derived from significantly better entropic contributions to binding displayed by the phenethyl-substituted imidazole compound.

Organizational Affiliation

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom.

Macromolecule Content

Total Structure Weight: 114.31 kDa
Atom Count: 8,998
Modeled Residue Count: 978
Deposited Residue Count: 978
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE A	A, B	489	Saccharolobus solfataricus	Mutation(s): 0 EC: 3.2.1.21 (PDB Primary Data), 3.2.1.23 (UniProt)
UniProt
Find proteins for P22498 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P22498 Go to UniProtKB: P22498
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22498
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGI Query on PGI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(5R,6R,7S,8S)-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL C₁₆ H₂₁ N₂ O₄ MLRMIFDEZCZOAE-APIJFGDWSA-O		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	D [auth A], E [auth A], G [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.246 (Depositor), 0.245 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.943	α = 90
b = 167.943	β = 90
c = 95.875	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-09-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-09-27
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description