SMTL ID : 5i8r.3 (2 other biounits)

aSMase with zinc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.65 Å

Oligo State

monomer

Ligands

1 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: 5 residues within 4Å: Chain A: I.472, N.474, T.476, Q.477, Q.488 No protein-ligand interaction detected (PLIP)

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 1 residues within 4Å: Chain A: N.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40 NAG.3: 1 residues within 4Å: Chain A: N.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129 NAG.4: 1 residues within 4Å: Chain A: N.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.349 NAG.5: 3 residues within 4Å: Chain A: P.325, Y.326, N.457 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.457

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.160, D.232, N.272, H.379, H.411 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.232, A:H.379, A:H.411 ZN.7: 6 residues within 4Å: Chain A: D.160, H.162, D.232, H.236, H.413 Ligands: ZN.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: 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
C

Sphingomyelin phosphodiesterase

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