SMTL ID : 2bf6.1

Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.97 Å

Oligo State

monomer

Ligands

1 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.1: 15 residues within 4Å: Chain A: R.24, I.25, R.43, D.49, I.85, D.86, F.111, F.218, Y.243, Q.251, E.297, R.313, Y.345, R.373, Y.413 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.25, A:I.85, A:F.218 Hydrogen bonds: A:R.24, A:R.43, A:D.49, A:D.49, A:D.86, A:Y.243, A:Q.251, A:E.297, A:R.313, A:Y.345, A:Y.413 Water bridges: A:E.297 Salt bridges: A:R.24, A:R.313, A:R.373

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.54, D.56, D.77, Y.78 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.54, A:D.77, A:Y.78, H2O.2, H2O.2 CA.3: 2 residues within 4Å: Chain A: D.273, W.331 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.273, A:W.331, H2O.12, H2O.12, H2O.12

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: K.309, T.323, T.334, E.336, Y.389, K.395, Y.396, E.397 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.309, A:T.323, A:E.336, A:Y.389, A:E.397, A:E.397 Water bridges: A:T.334, A:T.334, A:E.336, A:K.395 GOL.5: 6 residues within 4Å: Chain A: E.336, K.337, D.338, T.339, N.340, E.397 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.337, A:T.339, A:T.339, A:N.340 Water bridges: A:E.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newstead, S.L. et al., The Structure of Clostridium Perfringens Nani Sialidase and its Catalytic Intermediates. J.Biol.Chem. (2008)

Release Date

2006-03-09

Peptides

EXO-ALPHA-SIALIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

EXO-ALPHA-SIALIDASE