Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.09 kDa 
• Atom Count: 9031 
• Modelled Residue Count: 1004 
• Deposited Residue Count: 1008 
• Unique protein chains: 2

1H0I

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

• DOI: 10.2210/pdb1H0I/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Serratia marcescens, Gliocladium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-06-19 Released: 2002-06-27 
• Deposition Author(s): Houston, D.R., Shiomi, K., Arai, N., Omura, S., Peter, M.G., Turberg, A., Synstad, B., Eijsink, V.G.H., Aalten, D.M.F.

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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 

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

• PubMed: 12093900 
• DOI: 10.1073/pnas.132060599
• Primary Citation of Related Structures:  
  1H0I, 1H0G


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE B	A, B	499	Serratia marcescens	Mutation(s): 0  Gene Names: chiB EC: 3.2.1.14
Find proteins for P11797 (Serratia marcescens) Explore P11797  Go to UniProtKB:  P11797

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARGIFIN	C, D	5	Gliocladium	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEA	C,D	L-PEPTIDE LINKING	C10 H13 N O2		PHE
VR0	C,D	L-PEPTIDE LINKING	C8 H17 N5 O3		ARG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000465	C, D	Argifin	Oligopeptide /  Inhibitor		--

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 = 55.767	α = 90
b = 103.908	β = 90
c = 186.605	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-19 
• Released Date: 2002-06-27 
Deposition Author(s): Houston, D.R., Shiomi, K., Arai, N., Omura, S., Peter, M.G., Turberg, A., Synstad, B., Eijsink, V.G.H., Aalten, D.M.F.

Revision History  

• 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