SMTL ID : 5kky.1

Structure of Streptococcus pneumonia NanA bound with inhibitor 9N3Neu5Ac2en

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x 6UD: 5-acetamido-2,6-anhydro-3,5,9-trideoxy-9-triazan-1-yl-D-glycero-D-galacto-non-2-enonic acid(Non-covalent)

6UD.1: 16 residues within 4Å: Chain A: R.51, I.52, R.70, D.76, I.120, D.121, D.138, I.146, F.147, Y.294, Q.306, E.351, R.367, Y.399, R.425, Y.456 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.52, A:I.120 Hydrogen bonds: A:R.70, A:D.76, A:D.76, A:D.121, A:Q.306, A:E.351, A:R.367, A:Y.399, A:Y.399, A:Y.399, A:Y.456 Water bridges: A:R.51, A:Y.294, A:T.350 Salt bridges: A:R.51, A:R.367, A:R.425 6UD.4: 16 residues within 4Å: Chain B: R.51, I.52, R.70, D.76, I.120, D.121, D.138, I.146, Y.294, L.302, Q.306, E.351, R.367, Y.399, R.425, Y.456 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.120 Hydrogen bonds: B:R.70, B:D.76, B:D.121, B:Y.294, B:Q.306, B:Q.306, B:Q.306, B:E.351, B:R.367, B:Y.456 Water bridges: B:R.51, B:I.146, B:E.351, B:R.425 Salt bridges: B:R.51, B:R.367, B:R.425

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: G.220, N.221, K.228, T.229, S.230 Ligand excluded by PLIP CL.3: 6 residues within 4Å: Chain B: G.220, N.221, F.224, K.228, T.229, S.230 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slack, T.J. et al., Synthesis of selective inhibitors against S. pneumoniae and V. cholerae sialidases. To Be Published

Release Date

2017-06-28

Peptides

Sialidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sialidase A