5KKY | pdb_00005kky

Structure of Streptococcus pneumonia NanA bound with inhibitor 9N3Neu5Ac2en

• PDB DOI: https://doi.org/10.2210/pdb5KKY/pdb

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


• Deposited: 2016-06-23 Released: 2017-06-28 
• Deposition Author(s): Shi, D., Zhao, G.
• Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Synthesis of selective inhibitors against S. pneumoniae and V. cholerae sialidases

Slack, T.J., Zhao, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 111.98 kDa 
• Atom Count: 8,193 
• Modeled Residue Count: 941 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase A	A, B	496	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: nanA EC: 3.2.1.18
UniProt
Find proteins for P62575 (Streptococcus pneumoniae) Explore P62575  Go to UniProtKB:  P62575

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6UD	C [auth A], F [auth B]	5-acetamido-2,6-anhydro-3,5,9-trideoxy-9-triazan-1-yl-D-glycero-D-galacto-non-2-enonic acid C11 H20 N4 O7 FQISBZMFUOAQIB-UFGQHTETSA-N
CL	D [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.325	α = 90
b = 77.054	β = 98.52
c = 85.81	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Shi, D., Zhao, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	R01HD065122

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary