SMTL ID : 2vk6.1

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.56, A:D.77, H2O.3, H2O.3

1 x DAN: 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID(Non-covalent)

DAN.2: 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.25, A:I.85, A:F.218, A:Y.413 Hydrogen bonds: A:R.43, A:D.49, A:D.86, A:Y.243, A:Q.251, A:E.297, A:R.313, A:Y.413 Water bridges: A:R.373 Salt bridges: A:R.24, A:R.313, A:R.373

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: P.79, D.80, S.176 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: D.273, W.331 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.273, A:W.331, H2O.10, H2O.10, H2O.10, H2O.10 MG.5: 2 residues within 4Å: Chain A: V.10, G.66 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain A: S.177, T.178 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 2 residues within 4Å: Chain A: W.112, D.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.291

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

2008-01-22

Peptides

EXO-ALPHA-SIALIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

EXO-ALPHA-SIALIDASE

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