SMTL ID : 4xe9.1

Crystal structure of the NanB sialidase from Streptococcus pneumoniae in complex with Optactin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x OPX: (1s,3R,4S)-1-[(cyclohexylamino)methyl]-3,4-dihydroxycyclopentanesulfonic acid(Non-covalent)

OPX.1: 9 residues within 4Å: Chain A: Y.212, T.213, Q.456, K.461, I.558, T.619, E.620, L.621, P.622 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.212, A:T.213 Hydrogen bonds: A:T.213, A:T.213, A:T.213, A:Q.456 Water bridges: A:K.461, A:K.461, A:E.620 Salt bridges: A:K.461

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: L.46, F.67, R.69, E.77, Y.161 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.63 Salt bridges: A:E.77 pi-Cation interactions: A:F.67 DMS.3: 8 residues within 4Å: Chain A: R.91, V.128, Y.205, Y.269, R.272, H.642, L.643, S.644 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.91, A:S.644 DMS.4: 4 residues within 4Å: Chain A: Y.122, G.125, D.179, V.182 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.179 DMS.5: 4 residues within 4Å: Chain A: H.231, N.278, Q.280, R.638 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.638 Water bridges: A:R.638 pi-Cation interactions: A:H.231 DMS.6: 7 residues within 4Å: Chain A: V.347, G.351, I.366, N.367, D.368, Y.370, K.437 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rogers, G.W. et al., The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB. To be published

Release Date

2016-01-13

Peptides

Sialidase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sialidase B

Related Entries With Identical Sequence