SMTL ID : 8ub5.1

The Apo NanH structure from Clostridium perfringens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

14 x EDO: 1,2-ETHANEDIOL

EDO.1: 4 residues within 4Å: Chain A: N.108, D.185, G.186 Ligands: ACE.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.108 EDO.2: 8 residues within 4Å: Chain A: L.24, F.25, N.26, N.29, N.30, I.31, W.32, Y.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.26, A:I.31 EDO.3: 3 residues within 4Å: Chain A: K.27, D.28 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.27 Water bridges: A:D.28 EDO.4: 4 residues within 4Å: Chain A: D.185, G.186, T.187, K.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.186 EDO.5: 5 residues within 4Å: Chain A: Q.43, V.105, I.106, S.179, G.180 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.43, A:Q.43, A:I.106, A:S.179 Water bridges: A:V.182, A:K.354 EDO.6: 4 residues within 4Å: Chain A: D.47, G.48, T.49, T.75 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: L.276, G.278, K.305, T.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.278 Water bridges: A:N.306, A:T.307 EDO.8: 4 residues within 4Å: Chain A: K.35, G.60, P.61 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: T.129, T.131, R.132, R.133, S.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.134 EDO.10: 5 residues within 4Å: Chain A: K.308, N.315, P.338, K.339, D.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.308, A:N.315, A:P.338 Water bridges: A:D.340 EDO.11: 7 residues within 4Å: Chain A: T.292, N.294, H.296, I.298, D.322, I.380, K.382 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.294, A:N.294, A:H.296, A:K.382 EDO.12: 6 residues within 4Å: Chain A: L.44, L.45, N.46, G.48, K.354, N.355 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.46, A:G.48, A:N.355 EDO.13: 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:T.291 EDO.14: 5 residues within 4Å: Chain A: N.124, W.125, A.126, Y.204, S.230 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.124 Water bridges: A:W.125, A:Q.193, A:S.230

14 x ACE: ACETYL GROUP

ACE.15: 4 residues within 4Å: Chain A: L.237, R.297, F.323, L.326 No protein-ligand interaction detected (PLIP) ACE.16: 3 residues within 4Å: Chain A: K.305, N.315, I.335 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.305, A:I.335 ACE.17: 7 residues within 4Å: Chain A: Y.142, S.143, D.144, D.145, T.149, W.150, S.151 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.142 Hydrogen bonds: A:D.144, A:D.145 ACE.18: 5 residues within 4Å: Chain A: M.127, T.128, S.130, R.197, N.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.197 Water bridges: A:N.202 ACE.19: 4 residues within 4Å: Chain A: I.267, E.269, N.272, K.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.272 ACE.20: 3 residues within 4Å: Chain A: N.226, S.227, Y.247 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.226, A:Y.247 Hydrogen bonds: A:S.227 ACE.21: 3 residues within 4Å: Chain A: T.129, S.130, T.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.130, A:T.131 ACE.22: 4 residues within 4Å: Chain A: R.38, R.246, R.313, Y.348 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.348 Hydrogen bonds: A:R.246, A:R.246, A:R.313, A:R.313 ACE.23: 2 residues within 4Å: Chain A: I.288, K.289 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.288 Water bridges: A:S.179 ACE.24: 3 residues within 4Å: Chain A: T.109, G.110, D.144 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.111 ACE.25: 5 residues within 4Å: Chain A: N.226, Y.247, Y.252, I.267, N.272 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.267 Hydrogen bonds: A:Y.252, A:N.272 ACE.26: 7 residues within 4Å: Chain A: T.107, N.108, V.182, G.186, I.188, N.214 Ligands: EDO.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.108, A:V.182, A:I.188 Water bridges: A:N.214 ACE.27: 4 residues within 4Å: Chain A: Y.377, S.378, N.381, Q.383 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.377 Hydrogen bonds: A:N.381 ACE.28: 1 residues within 4Å: Chain A: K.212 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.212

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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