3OZP

Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with PUGNAc

• PDB DOI: https://doi.org/10.2210/pdb3OZP/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Ostrinia furnacalis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2010-09-27 Released: 2011-08-17 
• Deposition Author(s): Zhang, H., Liu, T., Liu, F., Shen, X., Yang, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Active-pocket size differentiating insectile from bacterial chitinolytic beta-N-acetyl-D-hexosaminidases

Liu, T., Zhang, H., Liu, F., Chen, L., Shen, X., Yang, Q.

(2011) Biochem J 438: 467-474

• PubMed: 21692744 
• DOI: https://doi.org/10.1042/BJ20110390
• Primary Citation of Related Structures:  
  3OZP, 3S6T


• PubMed Abstract: 
  

  Chitinolytic β-N-acetyl-D-hexosaminidase is a branch of the GH20 (glycoside hydrolase family 20) β-N-acetyl-D-hexosaminidases that is only distributed in insects and micro-organisms, and is therefore a potential target for the action of insecticides. PUGNAc [O-(2-acetamido-2-deoxy-D-glucopyransylidene)-amino-N-phenylcarbamate] was initially identified as an inhibitor against GH20 β-N-acetyl-D-hexosaminidases. So far no crystal structure of PUGNAc in complex with any GH20 β-N-acetyl-D-hexosaminidase has been reported. We show in the present study that the sensitivities of chitinolytic β-N-acetyl-D-hexosaminidases towards PUGNAc can vary by 100-fold, with the order being OfHex1 (Ostrinia furnacalis β-N-acetyl-D-hexosaminidase)

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Organizational Affiliation: 

School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 65.91 kDa 
• Atom Count: 5,253 
• Modelled Residue Count: 572 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylglucosaminidase	A	572	Ostrinia furnacalis	Mutation(s): 0  EC: 3.2.1.52
UniProt
Find proteins for Q06GJ0 (Ostrinia furnacalis) Explore Q06GJ0  Go to UniProtKB:  Q06GJ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAN	B [auth A]	O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N-PHENYLCARBAMATE C15 H19 N3 O7 PBLNJFVQMUMOJY-JXZOILRNSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OAN	PDBBind:  3OZP	Ki: 240 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.09	α = 90
b = 108.09	β = 90
c = 175.28	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Zhang, H., Liu, T., Liu, F., Shen, X., Yang, Q.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Non-polymer description
• Version 1.2: 2014-03-26
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary