SMTL ID : 4x4a.1

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with 2,7-Anhydro-Neu5Ac

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

1 x SKD: 2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID(Non-covalent)

SKD.1: 15 residues within 4Å: Chain A: R.23, I.24, R.42, D.48, I.104, D.105, D.122, S.130, Y.291, T.323, E.325, R.341, R.403, Y.443, W.464 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.42, A:D.105, A:R.341, A:Y.443 Water bridges: A:R.23, A:R.23, A:R.23, A:S.130, A:S.130, A:S.130, A:Y.291, A:T.323, A:R.341 Salt bridges: A:R.23, A:R.341, A:R.403

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: K.75, F.76, D.77, Y.103, E.186, N.188, N.222, Y.225, L.253 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.77, A:Y.103, A:E.186, A:E.186, A:N.188, A:N.222, A:Y.225 Water bridges: A:K.241 GOL.3: 7 residues within 4Å: Chain A: Y.242, S.243, D.244, D.245, T.249, W.250, S.251 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.243, A:D.244, A:D.245 Water bridges: A:D.244, A:T.249, A:T.249, A:D.252, A:D.252 GOL.4: 6 residues within 4Å: Chain A: S.8, G.64, K.65, Y.477, E.478, R.479 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.65, A:R.479, A:R.479 Water bridges: A:R.479

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 8 residues within 4Å: Chain A: E.297, N.318, G.320, A.322, T.342, G.343, S.344, R.362 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.297, A:E.297, A:N.318, A:G.343, A:G.343, A:S.344 Water bridges: A:G.320, A:G.320, A:R.362, A:R.362 Salt bridges: A:R.362

1 x ACE: ACETYL GROUP(Non-functional Binders)

ACE.6: 3 residues within 4Å: Chain A: S.360, E.361, K.421 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.361 Hydrogen bonds: A:E.361

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tailford, L.E. et al., Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation. Nat Commun (2015)

Release Date

2015-07-22

Peptides

Anhydrosialidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Anhydrosialidase

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