SMTL ID : 8ule.1

The structure of NanH in complex with Neu5,9Ac

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x 5N6: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid

5N6.1: 15 residues within 4Å: Chain A: R.38, I.39, R.57, D.63, M.100, D.101, W.119, N.124, W.125, A.126, Y.204, E.231, R.246, R.313, Y.348 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.119, A:W.125, A:A.126, A:Y.204 Hydrogen bonds: A:R.38, A:R.57, A:D.63, A:D.101, A:D.101, A:N.124, A:R.246 Water bridges: A:H.64, A:S.230, A:S.230 Salt bridges: A:R.38, A:R.246, A:R.313

14 x EDO: 1,2-ETHANEDIOL

EDO.2: 3 residues within 4Å: Chain A: N.108, D.185, G.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.108 EDO.3: 7 residues within 4Å: Chain A: L.24, F.25, N.26, N.29, N.30, I.31, Y.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.26, A:I.31 EDO.4: 5 residues within 4Å: Chain A: K.305, T.307, N.315, I.335 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.305, A:N.315 EDO.5: 3 residues within 4Å: Chain A: K.27, D.28 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.27 EDO.6: 4 residues within 4Å: Chain A: D.185, G.186, T.187, K.212 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: Q.43, V.105, I.106, S.179, G.180, V.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.43, A:Q.43, A:I.106, A:S.179 EDO.8: 3 residues within 4Å: Chain A: D.47, T.49, T.75 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: L.276, G.278, K.305, N.306, T.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.278, A:N.306 Water bridges: A:T.277 EDO.10: 4 residues within 4Å: Chain A: K.35, G.60, P.61 Ligands: EDO.5 No protein-ligand interaction detected (PLIP) EDO.11: 6 residues within 4Å: Chain A: N.226, Y.247, Y.252, Y.256, I.267, N.272 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.226, A:N.226, A:Y.252, A:Y.252, A:N.272 EDO.12: 4 residues within 4Å: Chain A: T.129, R.132, R.133, S.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.134, A:S.134 EDO.13: 7 residues within 4Å: Chain A: K.308, D.314, N.315, P.338, K.339, D.340 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.315, A:P.338 Water bridges: A:D.340 EDO.14: 6 residues within 4Å: Chain A: T.292, N.294, H.296, I.298, M.320, D.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.294, A:N.294, A:H.296 EDO.15: 6 residues within 4Å: Chain A: T.291, T.292, S.293, S.356, Y.377, N.381 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.377, A:N.381 Water bridges: A:S.356

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medley, B.J. et al., A "terminal" case of glycan catabolism: Structural and enzymatic characterization of the sialidases of Clostridium perfringens. J.Biol.Chem. (2024)

Release Date

2024-09-04

Peptides

Sialidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sialidase

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