1H0G

Complex of a chitinase with the natural product cyclopentapeptide argadin from Clonostachys


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

High Resolution Inhibited Complexes of a Chitinase with Natural Product Cyclopentapeptides - Peptide Mimicry of a Carbohydrate Substrate

Houston, D.R.Shiomi, K.Arai, N.Omura, S.Peter, M.G.Turberg, A.Synstad, B.Eijsink, V.G.H.Van Aalten, D.M.F.

(2002) Proc.Natl.Acad.Sci.USA 99: 9127

  • DOI: 10.1073/pnas.132060599
  • Primary Citation of Related Structures:  1H0I

  • PubMed Abstract: 
  • Over the past years, family 18 chitinases have been validated as potential targets for the design of drugs against human pathogens that contain or interact with chitin during their normal life cycles. Thus far, only one potent chitinase inhibitor has ...

    Over the past years, family 18 chitinases have been validated as potential targets for the design of drugs against human pathogens that contain or interact with chitin during their normal life cycles. Thus far, only one potent chitinase inhibitor has been described in detail, the pseudotrisaccharide allosamidin. Recently, however, two potent natural-product cyclopentapeptide chitinase inhibitors, argifin and argadin, were reported. Here, we describe high-resolution crystal structures that reveal the details of the interactions of these cyclopeptides with a family 18 chitinase. The structures are examples of complexes of a carbohydrate-processing enzyme with high-affinity peptide-based inhibitors and show in detail how the peptide backbone and side chains mimic the interactions of the enzyme with chitooligosaccharides. Together with enzymological characterization, the structures explain why argadin shows an order of magnitude stronger inhibition than allosamidin, whereas argifin shows weaker inhibition. The peptides bind to the chitinase in remarkably different ways, which may explain the differences in inhibition constants. The two complexes provide a basis for structure-based design of potent chitinase inhibitors, accessible by standard peptide chemistry.


    Organizational Affiliation

    Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHITINASE B
A, B
499Serratia marcescensGene Names: chiB
EC: 3.2.1.14
Find proteins for P11797 (Serratia marcescens)
Go to UniProtKB:  P11797
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ARGADIN
C, D
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002098
Query on PRD_002098
C,DArgadinCyclic peptide / Enzyme inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HSE
Query on HSE
C, D
L-PEPTIDE LINKINGC4 H9 N O3SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.063α = 90.00
b = 102.934β = 90.00
c = 185.784γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2013-08-07
    Type: Other
  • Version 1.4: 2015-09-16
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary