2VRJ

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

PDB DOI: https://doi.org/10.2210/pdb2VRJ/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli BL21
Mutation(s): No

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: 1.90 Å
R-Value Free: 0.239
R-Value Work: 0.195
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: https://doi.org/10.1002/cbic.200800451
Primary Citation of Related Structures:
2VRJ

Organizational Affiliation

Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Prof. García González 1, 41012 Sevilla, Spain.

Macromolecule Content

Total Structure Weight: 108.8 kDa
Atom Count: 8,070
Modelled Residue Count: 881
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE A	A, B	468	Thermotoga maritima	Mutation(s): 0 EC: 3.2.1.21
UniProt
Find proteins for Q08638 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q08638 Go to UniProtKB: Q08638
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08638
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCW Query on NCW Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth 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		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B]	E [auth A], F [auth A], I [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
NCW	PDBBind: 2VRJ	Kd: 500 (nM) from 1 assay(s)
NCW	Binding MOAD: 2VRJ	Kd: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.239
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.696	α = 90
b = 94.409	β = 90
c = 113.026	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-14

Deposition Author(s):

Garcia Fernandez, J.M.

Revision History (Full details and data files)

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Deposit Data

Help and Resources

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

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)