1O6I | pdb_00001o6i

Chitinase B from Serratia marcescens complexed with the catalytic intermediate mimic cyclic dipeptide CI4.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (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 0HZClick on this verticalbar to view details

This is version 1.6 of the entry. See complete history


Literature

The cyclic dipeptide CI-4 [cyclo-(l-Arg-d-Pro)] inhibits family 18 chitinases by structural mimicry of a reaction intermediate.

Houston, D.R.Eggleston, I.Synstad, B.Eijsink, V.G.van Aalten, D.M.

(2002) Biochem J 368: 23-27

  • DOI: https://doi.org/10.1042/BJ20021034
  • Primary Citation of Related Structures:  
    1O6I

  • PubMed Abstract: 

    Family 18 chitinases are attractive targets for the development of new inhibitors with chemotherapeutic potential against fungi, insects and protozoan/nematodal parasites. Although several inhibitors have been identified, these are based on complex chemistry, which hampers iterative structure-based optimization. Here we report the details of chitinase inhibition by the natural product peptide CI-4 [ cyclo -(L-Arg-D-Pro)], which possesses activity against the human pathogenic fungus Candida albicans, and describe a 1.7 A (0.17 nm) crystal structure of CI-4 in complex with the enzyme. The structure reveals that the cyclic dipeptide inhibits chitinases by structurally mimicking a reaction intermediate, and could, on the basis of its accessible chemistry, be a candidate for further optimization.


  • Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase
A, B
499Serratia marcescensMutation(s): 0 
Gene Names: chiB
EC: 3.2.1.14
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0HZ
Query on 0HZ

Download Ideal Coordinates CCD File 
C [auth A],
W [auth B]
amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium
C11 H20 N5 O2
ZRJHYOXNWCMGMW-JGVFFNPUSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
MA [auth B]
NA [auth B]
OA [auth B]
S [auth A]
T [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.805α = 90
b = 103.743β = 90
c = 186.283γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

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 0HZClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-30
    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: 2013-03-13
    Changes: Other
  • Version 1.4: 2018-06-13
    Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.6: 2024-11-13
    Changes: Structure summary