SMTL ID : 6er3.1

Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,3 sialyllactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

2 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.1: 10 residues within 4Å: Chain A: I.48, D.63, E.79, R.81, K.88, R.157, Y.163 Chain B: K.88 Ligands: GAL-SIA.2, GAL-SIA.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Water bridges: A:D.63, A:D.63, A:R.81, A:R.81, A:R.157, A:E.79, A:E.79, A:R.81, A:R.157 Hydrophobic interactions: A:I.48 Hydrogen bonds: A:K.88, A:K.88, A:Y.163, B:K.88 Salt bridges: A:R.81, A:R.157 GAL-SIA.2: 10 residues within 4Å: Chain A: K.88 Chain B: I.48, D.63, E.79, R.81, K.88, R.157, Y.163 Ligands: GAL-SIA.1, GAL-SIA.1 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Water bridges: B:D.63, B:R.81, B:R.81, B:R.157, B:R.81, B:R.157, B:R.157 Hydrophobic interactions: B:I.48 Hydrogen bonds: B:K.88, B:K.88, B:Y.163, B:Y.163, B:Y.163, A:K.88 Salt bridges: B:R.81, B:R.157

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain B: L.129, D.181 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Owen, C.D. et al., Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus. Nat Commun (2017)

Release Date

2018-05-02

Peptides

BNR/Asp-box repeat protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BNR/Asp-box repeat protein