7VRG | pdb_00007vrg

Crystal structure of chitinase-h from O. furnacalis in complex with Lynamicin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.243 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7U8Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Lynamicin B is a Potential Pesticide by Acting as a Lepidoptera-Exclusive Chitinase Inhibitor.

Lu, Q.Xu, L.Liu, L.Zhou, Y.Liu, T.Song, Y.Ju, J.Yang, Q.

(2021) J Agric Food Chem 69: 14086-14091

  • DOI: https://doi.org/10.1021/acs.jafc.1c05385
  • Primary Citation of Related Structures:  
    7VRG

  • PubMed Abstract: 

    Insect group h chitinase is a promising target for designing non-target safe pesticides in that it is exclusively distributed in lepidopteran insects, over 80% of which are agricultural pests. In this work, lynamicin B was discovered to be an inhibitor of Of Chi-h, the group h chitinase from the lepidopteran pest Ostrinia furnacalis . Lynamicin B was revealed to competitively inhibit Of Chi-h with a K i value of 8.76 μM and does not significantly inhibit other chitinases. The co-crystal structure of lynamicin B and Of Chi-h revealed that the dichloroindolyl group of lynamicin B occupies an unexplored pocket below subsites +1 and +2 of the substrate-binding cleft, which is vital for its selectivity. Feeding experiments demonstrated that lynamicin B exhibited high insecticidal activities against other lepidopteran pests Mythimna separata and Spodoptera frugiperda besides O. furnacalis . Moreover, lynamicin B did not affect Trichogramma ostriniae , a natural enemy of O. furnacalis . This study provides a natural-derived potent pesticide for the control of lepidopteran pests, leaving its natural enemy unaffected.


  • Organizational Affiliation

    School of Bioengineering, Dalian University of Technology, Dalian 116024, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase
A, B
540Ostrinia furnacalisMutation(s): 0 
Gene Names: OfChi-h
UniProt
Find proteins for Q4AE59 (Ostrinia furnacalis)
Explore Q4AE59 
Go to UniProtKB:  Q4AE59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4AE59
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth L],
D [auth C]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.908α = 113.634
b = 77.859β = 109.902
c = 81.972γ = 95
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7U8Click on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary