2WYN | pdb_00002wyn

Structure of family 37 trehalase from Escherichia coli in complex with a casuarine-6-O-a-D-glucoside analogue

PDB DOI: https://doi.org/10.2210/pdb2WYN/pdb

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

Deposited: 2009-11-17 Released: 2010-09-29
Deposition Author(s): Gloster, T.M., Roberts, S.M., Davies, G.J., Cardona, F., Goti, A., Parmeggiani, C., Parenti, P., Fusi, P., Forcella, M., Cipolla, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.209 (Depositor), 0.203 (DCC)
R-Value Work:
0.159 (Depositor)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Casuarine-6-O-alpha-D-glucoside and its analogues are tight binding inhibitors of insect and bacterial trehalases.

Cardona, F., Goti, A., Parmeggiani, C., Parenti, P., Forcella, M., Fusi, P., Cipolla, L., Roberts, S.M., Davies, G.J., Gloster, T.M.

(2010) Chem Commun (Camb) 46: 2629-2631

PubMed: 20461849 Search on PubMed
DOI: https://doi.org/10.1039/b926600c
Primary Citation Related Structures:
2WYN

PubMed Abstract:
Two novel casuarine-6-alpha-D-glucoside analogues, as well as the parent compound, were synthesized and tested as inhibitors towards Chironomus riparius, mammalian pig kidney and Escherichia coli trehalases. Their potent and selective activity is promising for the development of new insecticides.

Organizational Affiliation

Department of Chemistry U. Schiff, Laboratory of Design, Synthesis and Study of Biologically Active Heterocycles (HeteroBioLab), University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Florence, Italy. francesca.cardona@unifi.it

Macromolecule Content

Total Structure Weight: 246.82 kDa
Atom Count: 18,124
Modeled Residue Count: 2,013
Deposited Residue Count: 2,140
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC TREHALASE	A, B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13482
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LG9 Query on LG9 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain Q [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain Q [auth B]	AA [auth C], E [auth A], JA [auth D], Q [auth B]	(1R,2R,3R,6R,7R,7AR)-3,7-BIS(HYDROXYMETHYL)HEXAHYDRO-1H-PYRROLIZINE-1,2,6-TRIOL C₉ H₁₇ N O₅ WQQQECZSNNTNJJ-FJYMVOSHSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain Q [auth B]
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain F [auth A] SDF format, chain KA [auth D] SDF format, chain R [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain R [auth B]	BA [auth C], F [auth A], KA [auth D], R [auth B]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain BA [auth C] Focus chain F [auth A] Focus chain KA [auth D] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain F [auth A] Focus chain KA [auth D] Focus chain R [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain T [auth B] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain LA [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth C] SDF format, chain EA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] G [auth A] CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], PA [auth D], QA [auth D], RA [auth D], S [auth B], SA [auth D], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.209 (Depositor), 0.203 (DCC)
R-Value Work: 0.159 (Depositor)
R-Value Observed: 0.162 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.349	α = 90
b = 117.017	β = 90
c = 203.565	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

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Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-29
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: 2019-10-09
Changes: Data collection, Database references, Derived calculations, Other
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.6: 2024-10-16
Changes: Structure summary