SMTL ID : 5i8r.1 (2 other biounits)

aSMase with zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: T.242, R.243, N.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.243 NAG-NAG.2: 3 residues within 4Å: Chain A: D.123, N.349 Ligands: BMA.5 No protein-ligand interaction detected (PLIP)

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.3: 2 residues within 4Å: Chain A: W.38, N.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40 NAG.4: 1 residues within 4Å: Chain A: N.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129 NAG.6: 2 residues within 4Å: Chain A: Y.326, N.457 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.326 Hydrogen bonds: A:N.457 NAG.7: 6 residues within 4Å: Chain A: N.474, Q.477, Q.488, F.526, G.531 Ligands: NAG.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.526 Hydrogen bonds: A:N.474, A:Q.488 NAG.8: 2 residues within 4Å: Ligands: NAG.7, MAN.9 No protein-ligand interaction detected (PLIP)

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.5: 1 residues within 4Å: Ligands: NAG-NAG.2 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.9: 1 residues within 4Å: Ligands: NAG.8 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 6 residues within 4Å: Chain A: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.232, A:H.379, A:H.411 ZN.11: 5 residues within 4Å: Chain A: D.160, H.162, D.232, H.413 Ligands: ZN.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.160, A:D.232, A:H.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y.F. et al., Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease. Nat Commun (2016)

Release Date

2016-09-07

Peptides

Sphingomyelin phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sphingomyelin phosphodiesterase

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