8QK1 | pdb_00008qk1

Crystal structure of Trichuris suis beta-N-acetyl-D-hexosaminidase - HEX-2 in apo form

• PDB DOI: https://doi.org/10.2210/pdb8QK1/pdb

• Classification: HYDROLASE
• Organism(s): Trichuris suis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2023-09-14 Released: 2024-06-26 
• Deposition Author(s): Dutkiewicz, Z., Varrot, A.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.200 (DCC) 

Starting Model: in silico

Literature

Nematode hexosaminidases, a new biochemical tool for glycan analysis

Dutkiewicz, Z., Varrot, A., Wilson, I.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 63.33 kDa 
• Atom Count: 3,734 
• Modeled Residue Count: 456 
• Deposited Residue Count: 545 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-N-acetylhexosaminidase	A	545	Trichuris suis	Mutation(s): 0  Gene Names: M514_07548 EC: 3.2.1.52
UniProt
Find proteins for A0A085NCI8 (Trichuris suis) Explore A0A085NCI8  Go to UniProtKB:  A0A085NCI8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.200 (DCC) 

Diffraction Data: https://doi.org/10.5281/zenodo.8367522

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.118	α = 90
b = 59.044	β = 114.486
c = 105.977	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Dutkiewicz, Z., Varrot, A.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	W1224

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary