4FPO

Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 2-[(3-chloro-4-methoxybenzyl)ammonio]ethanesulfonate

• PDB DOI: https://doi.org/10.2210/pdb4FPO/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-22 Released: 2012-10-31 
• Deposition Author(s): Brear, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.268 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Synthesis and structural characterisation of selective non-carbohydrate-based inhibitors of bacterial sialidases.

Brear, P., Telford, J., Taylor, G.L., Westwood, N.J.

(2012) Chembiochem 13: 2374-2383

• PubMed: 23070966 
• DOI: https://doi.org/10.1002/cbic.201200433
• Primary Citation of Related Structures:  
  4FOQ, 4FOV, 4FOW, 4FOY, 4FP2, 4FP3, 4FPC, 4FPE, 4FPF, 4FPG, 4FPH, 4FPJ, 4FPK, 4FPL, 4FPO, 4FPY, 4FQ4


• PubMed Abstract: 
  

  The major human pathogen Streptococcus pneumoniae plays a key role in several disease states including septicaemia, meningitis and community-acquired pneumonia. Although vaccines against S. pneumoniae are available as prophylactics, there remains a need to identify and characterise novel chemical entities that can treat the diseases caused by this pathogen. S. pneumoniae expresses three sialidases, enzymes that cleave sialic acid from carbohydrate-based surface molecules. Two of these enzymes, NanA and NanB, have been implicated in the pathogenesis of S. pneumoniae and are considered to be validated drug targets. Here we report our studies on the synthesis and structural characterisation of novel NanB-selective inhibitors that are inspired by the β-amino-sulfonic acid family of buffers.

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Organizational Affiliation: 

Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.

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: 78.22 kDa 
• Atom Count: 5,466 
• Modelled Residue Count: 658 
• Deposited Residue Count: 697 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase B	A [auth B]	697	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: nanB, SP_1687 EC: 3.2.1.18
UniProt
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore Q54727  Go to UniProtKB:  Q54727

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LL9	B	2-[(3-chloro-4-methoxybenzyl)amino]ethanesulfonic acid C10 H14 Cl N O4 S BLSMHIDLTUGMQS-UHFFFAOYSA-N
DMS	C [auth B], D [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.268 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.457	α = 90
b = 82.487	β = 90
c = 116.807	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Brear, P.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations