8UM0

The structure of NanH in complex with Neu5,7,9Ac(2,6)-LAcNAc

• PDB DOI: https://doi.org/10.2210/pdb8UM0/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens ATCC 13124
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-17 Released: 2024-09-04 
• Deposition Author(s): Medley, B.J., Boraston, A.B.
• Funding Organization(s): Canadian Glycomics Network (GLYCONET)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

A terminal case of glycan catabolismstructural and enzymatic characterization of thesialidases of Clostridium perfringens

Medley, B.J., Low, K.E., Garber, J.M., Gray, T.E., Liu, L., Klassen, L., Fordwour, O.B., Inglis, G.D., Boons, G.J., Zandberg, W.F., Abbott, D.W.

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: 44.46 kDa 
• Atom Count: 3,036 
• Modelled Residue Count: 363 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase	A	383	Clostridium perfringens ATCC 13124	Mutation(s): 0  Gene Names: nanH
UniProt
Find proteins for B1V1R3 (Clostridium perfringens D str. JGS1721) Explore B1V1R3  Go to UniProtKB:  B1V1R3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X1F	C [auth A]	5-acetamido-7,9-di-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid C15 H23 N O11 NIHNZVQGPXTJRU-FSTWUICMSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.184	α = 90
b = 64.691	β = 102.75
c = 65.578	γ = 90

Software Package:

Software Name	Purpose
PHENIX	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., Boraston, A.B.

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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