SMTL ID : 9eot.1

Structure of human ceramide synthase 6 (CerS6) bound to C16:0 (nanobody Nb02)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x PLM: PALMITIC ACID(Covalent)

PLM.1: 14 residues within 4Å: Chain A: Y.189, H.211, S.215, I.219, S.222, V.230, G.231, L.235, H.238, R.275, T.287, Y.298, F.304, N.315 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.219, A:V.230, A:L.235, A:T.287, A:F.304, A:F.304 Hydrogen bonds: A:N.315 PLM.4: 14 residues within 4Å: Chain D: Y.189, H.211, S.215, I.219, S.222, V.230, G.231, L.235, H.238, R.275, T.287, Y.298, F.304, N.315 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.219, D:V.230, D:L.235, D:T.287, D:F.304, D:F.304 Hydrogen bonds: D:N.315

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 11 residues within 4Å: Chain A: L.5, F.8, W.9, W.21, A.35, L.38, Y.39, L.210, L.213, V.214, F.217 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.8, A:F.8, A:F.8, A:L.210, A:V.214, A:F.217, A:F.217 pi-Cation interactions: A:W.9, A:W.21 PC1.5: 11 residues within 4Å: Chain D: L.5, F.8, W.9, W.21, A.35, L.38, Y.39, L.210, L.213, V.214, F.217 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.8, D:F.8, D:F.8, D:L.210, D:V.214, D:F.217, D:F.217 pi-Cation interactions: D:W.9, D:W.21

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.18 NAG.6: 1 residues within 4Å: Chain D: N.18 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pascoa, T.C. et al., Structural basis of the mechanism and inhibition of a human ceramide synthase. Nature Structural & Molecular Biology (2024)

Release Date

2024-11-13

Peptides

Isoform 2 of Ceramide synthase 6: AD
Nanobody-02: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

C
D

Membrane

We predict this structure to be a membrane protein.
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Isoform 2 of Ceramide synthase 6

Nanobody-02

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