SMTL ID : 5hqn.1 (1 other biounit)

Catalytic domain of murine Acid Sphingomyelinase (ASMase, ASM, SMPD1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: 4 residues within 4Å: Chain A: S.132, R.133, T.166, N.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.133 NAG-NAG.3: 8 residues within 4Å: Chain A: N.336, I.362, N.364, T.366, Q.367, L.380, F.416, G.421 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 9 residues within 4Å: Chain A: S.16, F.175, I.238, N.239, T.241, D.242, P.243, A.244, G.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.244, A:G.245

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 9 residues within 4Å: Chain A: D.50, H.52, D.122, H.126, H.269, H.301, H.303 Ligands: ZN.5, PO4.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.50, A:H.52, A:D.122, A:H.303, H2O.1 ZN.5: 8 residues within 4Å: Chain A: D.50, D.122, N.162, H.163, H.269, H.301 Ligands: ZN.4, PO4.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.122, A:H.269, A:H.301, H2O.1

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 11 residues within 4Å: Chain A: D.50, H.52, D.122, H.126, N.162, H.163, H.269, H.301, H.303 Ligands: ZN.4, ZN.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.162 Water bridges: A:H.303 Salt bridges: A:H.52, A:H.126, A:H.163, A:H.301, A:H.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Crystal structure of mammalian acid sphingomyelinase. Nat Commun (2016)

Release Date

2016-07-06

Peptides

Sphingomyelin phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sphingomyelin phosphodiesterase

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