SMTL ID : 8j2f.1

Human neutral shpingomyelinase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: E.49 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.49, A:E.49 MG.5: 1 residues within 4Å: Chain B: E.49 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.49, B:E.49

2 x HP6: HEPTANE(Non-covalent)

HP6.2: 3 residues within 4Å: Chain A: P.104, F.371 Ligands: C14.3 No protein-ligand interaction detected (PLIP) HP6.6: 3 residues within 4Å: Chain B: P.104, F.371 Ligands: C14.4 No protein-ligand interaction detected (PLIP)

2 x C14: TETRADECANE(Non-covalent)

C14.3: 7 residues within 4Å: Chain A: W.112, L.373, F.374, Q.377 Chain B: W.112 Ligands: HP6.2, C14.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.112, A:L.373, A:L.373, A:F.374 C14.4: 5 residues within 4Å: Chain A: W.112 Chain B: W.112, Q.377 Ligands: C14.3, HP6.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yi, J. et al., Molecular basis for the catalytic mechanism of human neutral sphingomyelinases 1 (hSMPD2). Nat Commun (2023)

Release Date

2023-12-06

Peptides

Sphingomyelin phosphodiesterase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Sphingomyelin phosphodiesterase 2