9C20

The Sialidase NanJ in complex with Neu5,9Ac

• PDB DOI: https://doi.org/10.2210/pdb9C20/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-05-30 Released: 2024-09-04 
• Deposition Author(s): Medley, B.J., Low, K.E., Garber, J.M., Gray, T.E., Leeann, L.L., Fordwour, O.B., Inglis, G.D., Boons, G.J., Zandberg, W.F., Abbott, W., Boraston, A.
• Funding Organization(s): Canadian Glycomics Network (GLYCONET)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.184 

Starting Model: experimental

Literature

NanJ sialidase in complex with Neu5,9Ac

Medley, B.J., Boraston, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 50.69 kDa 
• Atom Count: 3,693 
• Modelled Residue Count: 451 
• Deposited Residue Count: 451 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exo-alpha-sialidase	A	451	Clostridium perfringens ATCC 13124	Mutation(s): 5  Gene Names: nanJ, CPF_0532 EC: 3.2.1.18
UniProt
Find proteins for A0A0H2YT71 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YT71  Go to UniProtKB:  A0A0H2YT71

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5N6 (Subject of Investigation/LOI)	C [auth A]	9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid C13 H21 N O10 NYWZBRWKDRMPAS-CTAKWSDESA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.254 
• R-Value Work: 0.184 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.037	α = 90
b = 171.037	β = 90
c = 93.296	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Medley, B.J., Low, K.E., Garber, J.M., Gray, T.E., Leeann, L.L., Fordwour, O.B., Inglis, G.D., Boons, G.J., Zandberg, W.F., Abbott, W., Boraston, A.

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Funding Organization	Location	Grant Number
Canadian Glycomics Network (GLYCONET)	Canada	--

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release