Macromolecule Content

Total Structure Weight: 108.43 kDa
Atom Count: 7733
Modelled Residue Count: 880
Deposited Residue Count: 936
Unique protein chains: 1

2JAL

Beta-glucosidase from Thermotoga maritima in complex with cyclophellitol

DOI: 10.2210/pdb2JAL/pdb

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

Deposited: 2006-11-29 Released: 2007-01-03
Deposition Author(s): Gloster, T.M., Madsen, R., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.244
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Basis for Cyclophellitol Inhibition of a Beta-Glucosidase.

Gloster, T.M., Madsen, R., Davies, G.J.

(2007) Org Biomol Chem 5: 444

PubMed: 17252125 Search on PubMed
DOI: 10.1039/b616590g
Primary Citation of Related Structures:
2JAL

PubMed Abstract:

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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YLL (Subject of Investigation/LOI) Query on YLL 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]	C [auth A], F [auth B]	(1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL C₇ H₁₄ O₆ QFYQIWDMMSKNFF-NYLBLOMBSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
YLL	PDBBind: 2JAL	Ki: 1.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.244
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.699	α = 90
b = 94.466	β = 90
c = 113.591	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2006-11-29
Released Date: 2007-01-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-01-03
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.