SMTL ID : 8t26.1

Crystal Structure of Porphyromonas gingivalis Sialidase (PG_0352) D219A mutant bound to 3'-Sialyllactose (only Neu5Ac visible)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

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

SIA.1: 14 residues within 4Å: Chain A: R.177, I.178, R.196, D.239, V.255, L.260, Q.269, F.310, D.364, E.365, R.381, Q.383, R.443, Y.471 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.178, A:V.255, A:F.310 Hydrogen bonds: A:R.196, A:D.239, A:E.365, A:R.381 Water bridges: A:R.177, A:R.196, A:Q.269, A:D.364, A:R.381, A:R.381 Salt bridges: A:R.177, A:R.381, A:R.443

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: R.303, W.306, L.355, S.356 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 8 residues within 4Å: Chain A: R.426, Q.431, L.450, D.452, R.457, W.458, S.459, F.505 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.431, A:S.455, A:A.460 PGE.4: 4 residues within 4Å: Chain A: S.321, G.322, R.323, D.347 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.321

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.5: 4 residues within 4Å: Chain A: K.48, Q.49, D.142, G.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.49, A:D.142 Water bridges: A:Q.49, A:D.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, N.D. et al., Functional and structural analyses reveal that a dual domain sialidase protects bacteria from complement killing through desialylation of complement factors. Plos Pathog. (2023)

Release Date

2023-10-04

Peptides

Sialidase, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sialidase, putative

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