1O6I | pdb_00001o6i

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

• PDB DOI: https://doi.org/10.2210/pdb1O6I/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-10-03 Released: 2003-03-30 
• Deposition Author(s): Houston, D.R., Eggleston, I., Synstad, B., Eijsink, V.G.H., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.195 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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

• PubMed: 12323074 
• DOI: https://doi.org/10.1042/BJ20021034
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 114.98 kDa 
• Atom Count: 9,538 
• Modeled Residue Count: 994 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0HZ	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	MA [auth B], NA [auth B], OA [auth B], S [auth A], T [auth A], U [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], V [auth A], X [auth B], Y [auth B], Z [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), 0.194 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.805	α = 90
b = 103.743	β = 90
c = 186.283	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-30 
Deposition Author(s): Houston, D.R., Eggleston, I., Synstad, B., Eijsink, V.G.H., van Aalten, D.M.F.

Revision History  

• 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