SMTL ID : 6er4.1

Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,6 sialyllactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-SIA.1: 14 residues within 4Å: Chain A: I.52, D.67, Y.73, E.83, R.85, D.88, K.92, R.161, Y.167 Chain B: I.52 Ligands: BGC-GAL-SIA.2, BGC-GAL-SIA.2, GOL.3, GOL.7 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.67, A:D.88, A:E.83, A:K.92, A:K.92, A:Y.167 Water bridges: A:D.67, A:R.85, A:R.85, A:D.88, A:D.88, A:R.85, A:E.83, A:R.85, A:R.161, A:R.161, A:R.161, A:Y.167 Hydrophobic interactions: A:I.52 Salt bridges: A:R.85, A:R.161 BGC-GAL-SIA.2: 14 residues within 4Å: Chain A: I.52 Chain B: I.52, D.67, Y.73, E.83, R.85, D.88, K.92, R.161, Y.167 Ligands: BGC-GAL-SIA.1, BGC-GAL-SIA.1, GOL.3, GOL.7 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.67, B:E.83, B:K.92, B:K.92, B:Y.167, B:Y.167 Water bridges: B:R.85, B:R.85, B:R.85, B:R.85, B:R.85, B:R.85, B:R.161, B:R.161, B:R.161, A:K.92 Hydrophobic interactions: B:I.52, B:Y.73 Salt bridges: B:R.85, B:R.161

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: I.52, Y.73, T.75, D.96 Chain B: D.88, K.92 Ligands: BGC-GAL-SIA.1, BGC-GAL-SIA.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.73, A:T.75, A:D.96, B:D.88 Hydrogen bonds: B:D.88 GOL.5: 3 residues within 4Å: Chain B: K.126, L.133, D.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.185 Water bridges: B:K.126, B:K.126 GOL.6: 6 residues within 4Å: Chain B: S.111, N.112, T.113, N.130, T.192, G.193 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.113, B:N.130, B:G.193 Water bridges: B:S.43, B:E.174 GOL.7: 8 residues within 4Å: Chain A: D.88, K.92 Chain B: I.52, Y.73, T.75, D.96 Ligands: BGC-GAL-SIA.1, BGC-GAL-SIA.2 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.73, A:D.88, A:D.88 Water bridges: B:Y.73, B:T.75, B:D.96, B:D.96, B:D.96, A:D.88, A:K.92

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 4 residues within 4Å: Chain A: T.19, G.20, Y.21, D.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.22 Water bridges: A:D.22, A:D.22, A:D.22

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