SMTL ID : 4xju.1

Crystal structure of the NanB sialidase from streptococcus pneumoniae in complex with 4-acetamido-2-fluoro-3-hydroxy-6-[1,2-dihydroxyethyl]-7,8-dioxabicyclo[3.2.1]octane-1-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

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

DMS.1: 4 residues within 4Å: Chain A: Y.212, T.213, Q.456, T.619 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.213, A:T.213, A:Q.456 Water bridges: A:E.620 pi-Cation interactions: A:Y.212 DMS.2: 7 residues within 4Å: Chain A: R.91, E.127, V.128, 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.3: 5 residues within 4Å: Chain A: D.113, D.116, A.176, I.177, S.178 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.113, A:D.116 DMS.4: 3 residues within 4Å: Chain A: N.338, D.410, L.412 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.338

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: K.60, N.61, R.79, R.155, Y.161 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.60, A:K.60, A:Y.63, A:Y.63 Salt bridges: A:K.60, A:R.79, A:R.155

1 x 19D: (1R,2R,3R,4R,5R,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-4-fluoro-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid(Non-covalent)

19D.6: 15 residues within 4Å: Chain A: R.207, I.208, R.226, D.232, I.288, D.289, D.306, N.314, Y.451, T.501, E.503, R.519, R.581, Y.615, W.636 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.451 Hydrogen bonds: A:R.226, A:D.289, A:N.314, A:T.501 Water bridges: A:R.207, A:R.519, A:R.581 Salt bridges: A:R.207, A:R.519, A:R.581 Halogen bonds: A:R.226

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