SMTL ID : 4x49.1

Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with oseltamivir carboxylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x G39: (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid(Non-covalent)

G39.1: 16 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 Ligands: GOL.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.443 Hydrogen bonds: A:R.42, A:D.48, A:Y.291, A:Y.291 Water bridges: A:D.48, A:A.49, A:S.130 Salt bridges: A:R.23, A:R.341, A:R.403

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: A.283 Ligands: GOL.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.283, H2O.1, H2O.6, H2O.10, H2O.13

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.23, D.48, S.463, W.464, R.466 Ligands: G39.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.23, A:D.48, A:W.464, A:R.466 Water bridges: A:R.42, A:D.48 GOL.4: 8 residues within 4Å: Chain A: K.75, F.76, D.77, Y.103, E.186, N.188, N.222, Y.225 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.77, A:D.77, A:Y.103, A:E.186, A:E.186 Water bridges: A:K.75, A:Y.225, A:K.241, A:K.241 GOL.5: 6 residues within 4Å: Chain A: G.402, K.404, Q.438, G.440, D.462, E.468 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.403, A:K.404, A:K.404, A:D.462 GOL.6: 7 residues within 4Å: Chain A: E.113, A.283, G.284, D.304, D.305, H.306 Ligands: CA.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.304, A:H.306 Water bridges: A:H.282, A:D.304

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

ACE.7: 2 residues within 4Å: Chain A: T.34, T.61 No protein-ligand interaction detected (PLIP) ACE.8: 5 residues within 4Å: Chain A: C.431, Y.432, S.433, V.487, P.489 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.487, A:P.489 Hydrogen bonds: A:S.433 ACE.9: 3 residues within 4Å: Chain A: E.453, R.479, E.484 No protein-ligand interaction detected (PLIP)

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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