Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 64782.71 
• Atom Count: 4655 
• Residue Count: 584 
• Unique protein chains: 1

3ARV

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with Sanguinarine

• DOI: 10.2210/pdb3ARV/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Vibrio harveyi
• Expression System: Escherichia coli


• Deposited: 2010-12-09 Released: 2011-04-20 
• Deposition Author(s): Pantoom, S., Vetter, I.R., Prinz, H., Suginta, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.177 
• R-Value Work: 0.144 

Literature

Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms

Pantoom, S., Vetter, I.R., Prinz, H., Suginta, W.

(2011) J.Biol.Chem. 286: 24312-24323

• PubMed: 21531720 
• DOI: 10.1074/jbc.M110.183376
• Primary Citation of Related Structures:  
  3AS3, 3AS2, 3AS1, 3AS0, 3ARZ, 3ARY, 3ARX, 3ARW, 3ARU, 3ART, 3ARS, 3ARR, 3ARQ, 3ARP, 3ARO


• PubMed Abstract: 
  

Six novel inhibitors of Vibrio harveyi chitinase A (VhChiA), a family-18 chitinase homolog, were identified by in vitro screening of a library of pharmacologically active compounds. Unlike the previously identified inhibitors that mimicked the reaction intermediates, crystallographic evidence from 14 VhChiA-inhibitor complexes showed that all of the inhibitor molecules occupied the outer part of the substrate-binding cleft at two hydrophobic areas. The interactions at the aglycone location are well defined and tightly associated with Trp-397 and Trp-275, whereas the interactions at the glycone location are patchy, indicating lower affinity and a loose interaction with two consensus residues, Trp-168 and Val-205. When Trp-275 was substituted with glycine (W275G), the binding affinity toward all of the inhibitors dramatically decreased, and in most structures two inhibitor molecules were found to stack against Trp-397 at the aglycone site. Such results indicate that hydrophobic interactions are important for binding of the newly identified inhibitors by the chitinase. X-ray data and isothermal microcalorimetry showed that the inhibitors occupied the active site of VhChiA in three different binding modes, including single-site binding, independent two-site binding, and sequential two-site binding. The inhibitory effect of dequalinium in the low nanomolar range makes this compound an extremely attractive lead compound for plausible development of therapeutics against human diseases involving chitinase-mediated pathologies.

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Related Citations: 

• Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism
  Songsiriritthigul, C.,Pantoom, S.,Aguda, A.H.,Robinson, R.C.,Suginta, W.
  (2008) J.Struct.Biol. 162: 491




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Organizational Affiliation: 

Biochemistry-Electrochemistry Research Unit, School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Chitinase A	A	584	Vibrio harveyi	Mutation(s): 0  Gene Names: chiA
Find proteins for Q9AMP1 (Vibrio harveyi) Go to UniProtKB:  Q9AMP1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SAU	A	13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium Sanguinarine C20 H14 N O4 INVGWHRKADIJHF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SAU	Kd: 2300 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.177 
• R-Value Work: 0.144 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 65.230	α = 90.00
b = 50.820	β = 99.49
c = 93.390	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-09 
• Released Date: 2011-04-20 
• Deposition Author(s): Pantoom, S., Vetter, I.R., Prinz, H., Suginta, W.

Revision History 

• Version 1.0: 2011-04-20
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2014-01-29
  Type: Database references