SMTL ID : 8qz7.1

Structure of human ceramide synthase 6 (CerS6) in complex with N-palmitoyl fumonisin B1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x XBX: (2~{R})-2-[2-[(5~{R},6~{R},7~{S},9~{S},11~{R},16~{R},18~{S},19~{S})-6-[(3~{R})-3-carboxy-5-oxidanyl-5-oxidanylidene-pentanoyl]oxy-19-(hexadecanoylamino)-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid(Non-covalent)

XBX.1: 29 residues within 4Å: Chain A: R.131, W.166, Y.189, H.211, H.212, S.215, L.218, I.219, S.222, M.227, V.230, G.231, V.234, L.235, H.238, D.242, L.245, K.249, N.252, Y.253, C.260, F.264, R.275, W.301, F.304, W.318, I.322, I.325, K.328 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.189, A:L.218, A:I.219, A:V.230, A:V.234, A:L.235, A:H.238, A:L.245, A:L.245, A:F.264, A:F.264, A:F.264, A:W.318, A:I.322 Hydrogen bonds: A:H.211, A:S.215, A:N.252, A:Y.253, A:R.275, A:R.275 Salt bridges: A:R.131, A:K.249, A:K.328 XBX.4: 29 residues within 4Å: Chain D: R.131, W.166, Y.189, H.211, H.212, S.215, L.218, I.219, S.222, M.227, V.230, G.231, V.234, L.235, H.238, D.242, L.245, K.249, N.252, Y.253, C.260, F.264, R.275, W.301, F.304, W.318, I.322, I.325, K.328 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:Y.189, D:L.218, D:I.219, D:V.230, D:V.234, D:L.235, D:H.238, D:L.245, D:L.245, D:F.264, D:F.264, D:F.264, D:W.318, D:I.322 Hydrogen bonds: D:H.211, D:S.215, D:N.252, D:Y.253, D:R.275, D:R.275 Salt bridges: D:R.131, D:K.249, D:K.328

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

PC1.2: 13 residues within 4Å: Chain A: L.5, F.8, W.9, W.21, A.35, E.36, L.38, Y.39, V.214, I.216, F.217, F.221, L.307 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.5, A:F.8, A:F.8, A:V.214, A:I.216, A:F.217, A:F.221, A:F.221, A:L.307 Hydrogen bonds: A:E.36, A:E.36 pi-Cation interactions: A:W.9, A:W.21 PC1.5: 13 residues within 4Å: Chain D: L.5, F.8, W.9, W.21, A.35, E.36, L.38, Y.39, V.214, I.216, F.217, F.221, L.307 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.5, D:F.8, D:F.8, D:V.214, D:I.216, D:F.217, D:F.221, D:F.221, D:L.307 Hydrogen bonds: D:E.36, D:E.36 pi-Cation interactions: D:W.9, D:W.21

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

NAG.3: 2 residues within 4Å: Chain A: N.18 Chain B: N.74 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.74, A:N.18 NAG.6: 2 residues within 4Å: Chain C: N.74 Chain D: N.18 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.18, C:N.74

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-22: 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-22

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