SMTL ID : 8ijq.1

The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x 16C: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE(Non-covalent)

16C.1: 12 residues within 4Å: Chain A: F.20, M.27, G.65, M.93, F.97, R.100, F.140, M.142, D.152, G.157, H.158, V.161 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.20, A:F.97, A:V.161, A:V.161 Hydrogen bonds: A:R.100, A:R.100, A:F.140, A:D.152 16C.2: 12 residues within 4Å: Chain B: F.20, S.24, M.27, M.93, F.97, R.100, F.140, M.142, D.152, G.157, H.158, V.161 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.20, B:F.97, B:V.161, B:V.161 Hydrogen bonds: B:R.100, B:R.100, B:D.152 16C.3: 12 residues within 4Å: Chain C: F.20, M.27, E.62, G.65, M.66, C.69, R.100, F.140, D.152, G.157, H.158, V.161 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.20, C:F.140, C:V.161 Hydrogen bonds: C:R.100, C:R.100, C:D.152, C:D.152 16C.4: 13 residues within 4Å: Chain D: F.20, G.65, M.66, C.69, M.93, F.97, R.100, F.140, M.142, D.152, G.157, H.158, V.161 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.20, D:F.97, D:F.140, D:V.161, D:V.161 Hydrogen bonds: D:R.100, D:R.100, D:D.152, D:H.158, D:H.158 16C.5: 10 residues within 4Å: Chain E: F.20, M.27, F.97, R.100, F.140, M.142, D.152, G.157, H.158, V.161 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.97, E:V.161 Hydrogen bonds: E:R.100, E:R.100, E:D.152, E:D.152, E:H.158 16C.6: 12 residues within 4Å: Chain F: F.20, M.27, M.66, C.69, L.89, R.100, F.140, M.142, D.152, G.157, H.158, V.161 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:F.20, F:F.20, F:L.89, F:V.161 Hydrogen bonds: F:R.100, F:R.100, F:G.141, F:D.152, F:D.152, F:H.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, K. et al., Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-02-28

Peptides

Sphingomyelin synthase-related protein 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Sphingomyelin synthase-related protein 1

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