Molecular Basis for Beta-Glucosidase Inhibition by Ring-Modified Calystegine Analogues.

Aguilar, M.; Gloster, T.M.; Garcia-Moreno, M.I.; Ortiz Mellet, C.; Davies, G.J.; Llebaria, A.; Casas, J.; Egido-Gabas, M.; Garcia Fernandez, J.M.

doi:10.2210/pdb2vrj/pdb

Macromolecule Content

Total Structure Weight: 108803.50
Atom Count: 7401
Residue Count: 936
Unique protein chains: 1

2VRJ

Beta-glucosidase from Thermotoga maritima in complex with N-octyl-5- deoxy-6-oxa-N-(thio)carbamoylcalystegine

DOI: 10.2210/pdb2VRJ/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Expression System: Escherichia coli BL21

Deposited: 2008-04-09 Released: 2008-10-14
Deposition Author(s): Aguilar, M., Gloster, T.M., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Llebaria, A., Casas, J., Egido-Gabas, M., Garcia Fernandez, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.9 Å
R-Value Free: 0.239
R-Value Work: 0.195

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular Basis for Beta-Glucosidase Inhibition by Ring-Modified Calystegine Analogues.

Aguilar, M., Gloster, T.M., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Llebaria, A., Casas, J., Egido-Gabas, M., Garcia Fernandez, J.M.

(2008) Chembiochem 9: 2612

PubMed: 18833549 Search on PubMed
DOI: 10.1002/cbic.200800451

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BETA-GLUCOSIDASE A	A, B	468	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)	Mutation(s): 0 Gene Names: bglA EC: 3.2.1.21
Find proteins for Q08638 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)) Go to UniProtKB: Q08638
Protein Feature View Full Protein Feature View for Q08638

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
ACT Query on ACT Download SDF File Download CCD File	A, B	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
CA Query on CA Download SDF File Download CCD File	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction
NCW Query on NCW Download SDF File Download CCD File	A, B	(1S,2R,3S,4R,5R)-2,3,4-trihydroxy-N-octyl-6-oxa-8-azabicyclo[3.2.1]octane-8-carbothioamide C₁₅ H₂₈ N₂ O₄ S LFSNQOFOMJLHIW-MEBFFEOJSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
NCW	Ki: 280 nM BINDINGMOAD
NCW	Kd: 500 nM PDBBIND

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.9 Å
R-Value Free: 0.239
R-Value Work: 0.195
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 93.696	α = 90.00
b = 94.409	β = 90.00
c = 113.026	γ = 90.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2008-04-09
Released Date: 2008-10-14
Deposition Author(s): Aguilar, M., Gloster, T.M., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Llebaria, A., Casas, J., Egido-Gabas, M., Garcia Fernandez, J.M.

Revision History

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Type: Advisory, Version format compliance

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

148969 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

2VRJ

Beta-glucosidase from Thermotoga maritima in complex with N-octyl-5- deoxy-6-oxa-N-(thio)carbamoylcalystegine

Molecular Basis for Beta-Glucosidase Inhibition by Ring-Modified Calystegine Analogues.

Entity ID: 1

Experimental Data

Structure Validation

Deposition Data

Revision History