SMTL ID : 8ijr.1

The cryo-EM structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x Z0P: (2S)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11Z)-octadec-11-enoate(Non-covalent)

Z0P.1: 16 residues within 4Å: Chain A: F.163, M.170, C.212, L.232, M.236, F.240, R.243, I.279, F.283, M.285, H.291, D.295, G.300, H.301, V.304 Ligands: OPE.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.163, A:F.163, A:F.163, A:L.232, A:F.240 Hydrogen bonds: A:D.295 Salt bridges: A:R.243, A:H.301 Z0P.3: 18 residues within 4Å: Chain B: F.160, F.163, M.170, G.208, C.212, L.232, M.236, F.240, R.243, I.279, F.283, M.285, H.291, D.295, G.300, H.301, V.304 Ligands: OPE.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.160, B:F.163, B:F.163, B:F.163, B:L.232, B:F.240, B:V.304 Hydrogen bonds: B:D.295 Salt bridges: B:R.243, B:H.301 Z0P.5: 15 residues within 4Å: Chain C: F.163, S.167, M.170, G.208, C.212, W.215, L.216, L.219, L.232, R.243, I.279, F.283, D.295, G.300, H.301 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.163, C:F.163, C:L.216, C:L.219, C:L.232, C:F.283 Hydrogen bonds: C:D.295, C:G.300 Salt bridges: C:R.243, C:H.301 Z0P.6: 14 residues within 4Å: Chain D: F.163, M.170, G.208, C.212, L.229, L.232, F.240, R.243, I.279, F.283, M.285, D.295, H.301, V.304 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.163, D:F.163, D:F.163, D:L.229, D:F.240, D:V.304, D:V.304 Hydrogen bonds: D:D.295 Salt bridges: D:R.243, D:H.301 Z0P.7: 15 residues within 4Å: Chain E: F.163, M.170, G.208, C.212, L.229, L.232, C.233, M.236, R.243, I.279, F.283, M.285, D.295, H.301, V.304 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.163, E:F.163, E:L.232, E:V.304, E:V.304 Hydrogen bonds: E:D.295, E:H.301 Salt bridges: E:R.243, E:H.301 Z0P.8: 12 residues within 4Å: Chain F: F.163, S.167, M.170, G.208, M.209, C.212, L.216, R.243, F.283, D.295, H.301, V.304 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.216, F:F.283, F:V.304 Hydrogen bonds: F:D.295 Salt bridges: F:R.243, F:H.301

2 x OPE: PHOSPHORIC ACID MONO-(2-AMINO-ETHYL) ESTER(Non-covalent)

OPE.2: 9 residues within 4Å: Chain A: M.170, H.174, R.275, V.290, H.291, T.292, C.293, G.294 Ligands: Z0P.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.275, A:V.290, A:T.292 Salt bridges: A:H.291 OPE.4: 9 residues within 4Å: Chain B: M.170, I.279, V.290, H.291, T.292, C.293, G.294, D.295 Ligands: Z0P.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.275, B:R.275, B:T.292, B:C.293, B:D.295 Salt bridges: B:H.291

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