Two copies of the catalytic domain of nana sialidase from streptococcus pneumoniae juxtaposed in the P212121 space group, in complex with dana derivatized with a peg linker on the glycerol group.

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 45% strand (DSSP).

Ligands and binding sites

• R7H · (4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{S})-3-[[1-(2-ethoxyethyl)-1,2,3-triazol-4-yl]methylsulfanyl]-1, 2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid · ligand · 2 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, B
• CL · Chloride ion · ion · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1264 Ų buried · 22 hydrogen bonds · protein-protein

Compared structures

• 7A5X · Two copies of the catalytic domain of NanA sialidase from Streptococcus pneumoniae… · the same entry in another collection · chain A against A, TM-score 1.00
• P62575 · AlphaFold monomer V2.0 prediction for sialidase a (P62575) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P62575
• Elsewhere: RCSB PDB 7A5X · PDBe 7A5X · UniProt P62575