Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 42.17 kDa 
• Atom Count: 3213 
• Modelled Residue Count: 364 
• Deposited Residue Count: 364 
• Unique protein chains: 1

1HKK

High resoultion crystal structure of human chitinase in complex with allosamidin

• PDB DOI: 10.2210/pdb1HKK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2003-03-10 Released: 2004-03-11 
• Deposition Author(s): Rao, F.V., Houston, D.R., Boot, R.G., Aerts, J.M.F.G., Sakuda, S., Van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.189 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase.

Rao, F.V., Houston, D.R., Boot, R.G., Aerts, J.M.F.G., Sakuda, S., Van Aalten, D.M.F.

(2003) J Biol Chem 278: 20110

• PubMed: 12639956 
• DOI: 10.1074/jbc.M300362200
• Primary Citation of Related Structures:  
  1HKI, 1HKJ, 1HKK, 1HKM


• PubMed Abstract: 
  

The pseudotrisaccharide allosamidin is a potent family 18 chitinase inhibitor with demonstrated biological activity against insects, fungi, and the Plasmodium falciparum life cycle. The synthesis and biological properties of several derivatives have been reported. The structural interactions of allosamidin with several family 18 chitinases have been determined by x-ray crystallography previously. Here, a high resolution structure of chitotriosidase, the human macrophage chitinase, in complex with allosamidin is presented. In addition, complexes of the allosamidin derivatives demethylallosamidin, methylallosamidin, and glucoallosamidin B are described, together with their inhibitory properties. Similar to other chitinases, inhibition of the human chitinase by allosamidin derivatives lacking a methyl group is 10-fold stronger, and smaller effects are observed for the methyl and C3 epimer derivatives. The structures explain the effects on inhibition in terms of altered hydrogen bonding and hydrophobic interactions, together with displaced water molecules. The data reported here represent a first step toward structure-based design of specific allosamidin derivatives.

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Organizational Affiliation: 

Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Scotland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITOTRIOSIDASE-1	A	364	Homo sapiens	Mutation(s): 0  Gene Names: CHIT1 EC: 3.2.1.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q13231 (Homo sapiens) Explore Q13231  Go to UniProtKB:  Q13231
PHAROS:  Q13231 GTEx:  ENSG00000133063

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-allopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-allopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan:  G77950XB GlyCosmos:  G77950XB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMI	D [auth A], E [auth A]	ALLOSAMIZOLINE C9 H16 N2 O4 MKJAYSJDHSEFRI-PVFLNQBWSA-N
ZN	F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.189 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.858	α = 90
b = 94.858	β = 90
c = 83.483	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-10 
• Released Date: 2004-03-11 
Deposition Author(s): Rao, F.V., Houston, D.R., Boot, R.G., Aerts, J.M.F.G., Sakuda, S., Van Aalten, D.M.F.

Revision History  

• Version 1.0: 2004-03-11
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary