Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 64547.54 
• Atom Count: 4498 
• Residue Count: 584 
• Unique protein chains: 1

3ARU

Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant complex structure with PENTOXIFYLLINE

• DOI: 10.2210/pdb3ARU/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Vibrio harveyi
• Expression System: Escherichia coli
• Mutation(s): 1 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.195 
• R-Value Work: 0.143 

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, 3ARV, 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.

---

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




---

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): 1  Gene Names: chiA
Find proteins for Q9AMP1 (Vibrio harveyi) Go to UniProtKB:  Q9AMP1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PNX	A	3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE PENTOXIFYLLINE C13 H18 N4 O3 BYPFEZZEUUWMEJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PNX	Kd: 600000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.195 
• R-Value Work: 0.143 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 66.670	α = 90.00
b = 83.930	β = 90.00
c = 102.420	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

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