2JKB

Crystal structure of Streptococcus pneumoniae NanB in complex with 2, 7-anhydro-Neu5Ac

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structural and Functional Studies of Streptococcus Pneumoniae Neuraminidase B: An Intramolecular Trans-Sialidase.

Gut, H., King, S.J., Walsh, M.A.

(2008) FEBS Lett 582: 3348

  • DOI: https://doi.org/10.1016/j.febslet.2008.08.026
  • Primary Citation of Related Structures:  
    2JKB

  • PubMed Abstract: 

    The human pathogen Streptococcus pneumoniae expresses neuraminidase proteins that cleave sialic acids from complex carbohydrates. The pneumococcus genome encodes up to three neuraminidase proteins that have been shown to be important virulence factors. Here, we report the first structure of a neuraminidase from S. pneumoniae: the crystal structure of NanB in complex with its reaction product 2,7-anhydro-Neu5Ac. Our structural data, together with biochemical analysis, establish NanB as an intramolecular trans-sialidase with strict specificity towards alpha2-3 linked sialic acid substrates. In addition, we show that NanB differs in its substrate specificity from the other pneumococcal neuraminidase NanA.

    • Organizational Affiliation: 

    MRC France, BM14 c/o ESRF, 6 rue Jules Horowitz, BP220, 38043 Grenoble, France.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIALIDASE B686Streptococcus pneumoniae TIGR4Mutation(s): 0 
EC: 4.2.2.15 (PDB Primary Data), 3.2.1.18 (UniProt)
UniProt
Find proteins for Q54727 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q54727 
Go to UniProtKB:  Q54727
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54727
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SKD
Query on SKD
Download Ideal Coordinates CCD File 
B [auth A]2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID
C11 H17 N O8
NCMJSVDTRDLWJE-YRMXFSIDSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.719α = 90
b = 82.746β = 90
c = 118.079γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Other, Refinement description