1H0I

Complex of a chitinase with the natural product cyclopentapeptide argifin from Gliocladium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 3.0 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 U S A 99: 9127

  • DOI: 10.1073/pnas.132060599
  • Primary Citation of Related Structures:  
    1H0G, 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 been described in detail, the pseudotrisaccharide allosamidin ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHITINASE BA, B499Serratia marcescensMutation(s): 0 
Gene Names: chiB
EC: 3.2.1.14
Membrane Entity: Yes 
UniProt
Find proteins for P11797 (Serratia marcescens)
Explore P11797 
Go to UniProtKB:  P11797
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11797
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ARGIFINC, D5GliocladiumMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
U [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MEA
Query on MEA
C, D L-PEPTIDE LINKINGC10 H13 N O2PHE
VR0
Query on VR0
C, D L-PEPTIDE LINKINGC8 H17 N5 O3ARG
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000465
Query on PRD_000465
C, DArgifinOligopeptide / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.767α = 90
b = 103.908β = 90
c = 186.605γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 1.3: 2017-08-30
    Changes: Advisory, Data collection
  • Version 2.0: 2023-01-25
    Changes: Atomic model, Database references, Derived calculations, Other
  • Version 3.0: 2023-03-15
    Changes: Atomic model