2JF4

Family 37 trehalase from Escherichia coli in complex with validoxylamine

PDB DOI: https://doi.org/10.2210/pdb2JF4/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-01-25 Released: 2007-02-13
Deposition Author(s): Gibson, R.P., Gloster, T.M., Roberts, S., Warren, R.A.J., Storch De Gracia, I., Garcia, A., Chiara, J.L., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.214
R-Value Work: 0.163
R-Value Observed: 0.166

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 Trehalase Inhibition Revealed by the Structure of Trehalase in Complex with Potent Inhibitors.

Gibson, R.P., Gloster, T.M., Roberts, S., Warren, R.A.J., Storch De Gracia, I., Garcia, A., Chiara, J.L., Davies, G.J.

(2007) Angew Chem Int Ed Engl 46: 4115

PubMed: 17455176 Search on PubMed
DOI: https://doi.org/10.1002/anie.200604825
Primary Citation of Related Structures:
2JF4, 2JG0

Organizational Affiliation

Department of Chemistry, York Structural Biology Laboratory, York, YO, UK.

Macromolecule Content

Total Structure Weight: 61.52 kDa
Atom Count: 4,338
Modelled Residue Count: 500
Deposited Residue Count: 535
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC TREHALASE	A	535	Escherichia coli K-12	Mutation(s): 0 EC: 3.2.1.28
UniProt
Find proteins for P13482 (Escherichia coli (strain K12)) Explore P13482 Go to UniProtKB: P13482
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13482
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VDM Query on VDM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL C₁₄ H₂₅ N O₈ YCJYNBLLJHFIIW-MBABXGOBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
VDM	PDBBind: 2JF4	Kd: 7 (nM) from 1 assay(s)
VDM	Binding MOAD: 2JF4	Kd: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.214
R-Value Work: 0.163
R-Value Observed: 0.166
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.399	α = 90
b = 102.696	β = 90
c = 103.174	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Storch De Gracia, I.

Revision History (Full details and data files)

Version 1.0: 2007-02-13
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 Core Operations are 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.