SMTL ID : 5fic.1 (3 other biounits)

Open form of murine Acid Sphingomyelinase in presence of lipid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 9 residues within 4Å: Chain A: N.417, I.443, N.445, T.447, Q.448, K.459, L.461, F.497, G.502 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: 10 residues within 4Å: Chain A: W.99, N.100, I.101, F.256, N.320, T.322, D.323, P.324, A.325, G.326 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.322 Hydrogen bonds: A:G.326

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 8 residues within 4Å: Chain A: D.131, H.133, D.203, H.350, H.382, H.384 Ligands: ZN.4, PO4.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.131, A:H.133, A:D.203, A:H.384 ZN.4: 8 residues within 4Å: Chain A: D.131, D.203, N.243, H.244, H.350, H.382 Ligands: ZN.3, PO4.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.203, A:H.350, A:H.382

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

PO4.5: 11 residues within 4Å: Chain A: D.131, H.133, D.203, H.207, N.243, H.244, H.382, H.384, F.413 Ligands: ZN.3, ZN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.243 Salt bridges: A:H.133, A:H.207, A:H.244, A:H.382, A:H.384 PO4.6: 4 residues within 4Å: Chain A: V.123, S.124, R.125, Q.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.424 Salt bridges: A:R.125 PO4.7: 8 residues within 4Å: Chain A: W.362, L.397, R.525, D.527, S.528, P.529, A.530, L.531 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.528, A:A.530 Salt bridges: A:R.525

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 1 residues within 4Å: Chain A: R.399 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: Y.138, L.139, E.140, R.180 Ligand excluded by PLIP

1 x 6E0: octadecylphosphonic acid(Non-covalent)

6E0.10: 11 residues within 4Å: Chain A: L.20, F.21, A.23, L.24, H.26, G.27, L.28, N.33, V.37, L.76, L.85 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.20, A:L.24, A:L.28, A:V.37 Hydrogen bonds: A:G.27

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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