› 2jkb

X-ray diffraction
1.54Å resolution

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

Released:
DOI: 10.2210/pdb2jkb/pdb
PDB entry 2jkb coloured by chain, front view.
PDB entry 2jkb coloured by chain, side view.
PDB entry 2jkb coloured by chain, top view.
Source organism: Streptococcus pneumoniae TIGR4
Primary publication:
Structural and functional studies of Streptococcus pneumoniae neuraminidase B: An intramolecular trans-sialidase.
Gut H, King SJ, Walsh MA
FEBS Lett 582 3348-52 (2008)
PMID: 18775704

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176218 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sialidase B Chain: A
Molecule details ›
Chain: A
Length: 686 amino acids
Theoretical weight: 76.74 KDa
Source organism: Streptococcus pneumoniae TIGR4
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q54727 (Residues: 22-29, 30-697; Coverage: 100%)
Gene names: SP_1687, nanB
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SKD 1 x SKD
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P212121
Unit cell:
a: 76.719Å b: 82.746Å c: 118.079Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.162 0.188
Expression system: Escherichia coli BL21

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Citations

10 review citations

Carbohydrate-binding domains: multiplicity of biological roles.
Guillén et al. (2010)
9 more

2 mentions without citation

Dual Acting Neuraminidase Inhibitors Open New Opportunities to Disrupt the Lethal Synergism between Streptococcus pneumoniae and Influenza Virus.
Walther et al. (2016)
1 more