SMTL ID : 8zb1.1

Cryo-EM structure of the C26-FB1-bound Lac1-Lip1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

6 x 6PL: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

6PL.1: 7 residues within 4Å: Chain A: K.128, G.129, L.260, L.261, W.264 Chain B: I.34, E.38 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.128, A:L.260, A:L.261, A:W.264, B:I.34 6PL.2: 13 residues within 4Å: Chain A: H.111, V.114, A.115, F.135, Y.139, F.143, Y.182, S.186, F.189, F.218, V.222, G.226, Q.227 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.115, A:F.135, A:Y.139, A:F.143, A:Y.182, A:F.189, A:F.218 6PL.4: 10 residues within 4Å: Chain A: F.269 Chain B: A.36, F.40, G.43, N.47, W.50, F.51, K.86, R.90 Chain D: Y.39 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.40, B:F.40, B:F.40, A:F.269, A:F.269 Salt bridges: B:K.86, B:R.90 6PL.5: 7 residues within 4Å: Chain C: K.128, G.129, L.260, L.261, W.264 Chain D: I.34, E.38 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:K.128, C:L.260, C:L.261, C:W.264, D:I.34 6PL.6: 13 residues within 4Å: Chain C: H.111, V.114, A.115, F.135, Y.139, F.143, Y.182, S.186, F.189, F.218, V.222, G.226, Q.227 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.115, C:F.135, C:Y.139, C:F.143, C:Y.182, C:F.189, C:F.218 6PL.8: 10 residues within 4Å: Chain B: Y.39 Chain C: F.269 Chain D: A.36, F.40, G.43, N.47, W.50, F.51, K.86, R.90 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.269, C:F.269, D:F.40, D:F.40, D:F.40 Salt bridges: D:K.86, D:R.90

2 x 01: (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-(hexacosanoylamino)-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid

01.3: 33 residues within 4Å: Chain A: Y.224, W.231, L.252, H.255, T.259, L.262, I.263, S.265, S.266, F.269, F.271, G.275, I.278, Y.279, M.282, D.286, L.289, N.296, Y.297, F.304, F.307, R.318, L.341, Y.348, C.350, I.352, S.353, V.357, W.371, L.374, I.375, V.378, R.385 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:T.259, A:L.262, A:I.263, A:F.269, A:F.271, A:F.271, A:I.278, A:I.278, A:Y.279, A:Y.279, A:M.282, A:L.289, A:F.307, A:L.341, A:Y.348, A:I.352, A:V.357, A:W.371, A:W.371, A:I.375, A:V.378 Hydrogen bonds: A:H.255, A:N.296, A:Y.297 Salt bridges: A:K.293, A:K.293, A:R.381, A:R.385, A:R.385 01.7: 33 residues within 4Å: Chain C: Y.224, W.231, L.252, H.255, T.259, L.262, I.263, S.265, S.266, F.269, F.271, G.275, I.278, Y.279, M.282, D.286, L.289, N.296, Y.297, F.304, F.307, R.318, L.341, Y.348, C.350, I.352, S.353, V.357, W.371, L.374, I.375, V.378, R.385 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:T.259, C:L.262, C:I.263, C:F.269, C:F.271, C:F.271, C:I.278, C:I.278, C:Y.279, C:Y.279, C:M.282, C:L.289, C:F.307, C:L.341, C:Y.348, C:I.352, C:V.357, C:W.371, C:W.371, C:I.375, C:V.378 Hydrogen bonds: C:H.255, C:N.296, C:Y.297 Salt bridges: C:K.293, C:K.293, C:R.381, C:R.385, C:R.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Mechanism of ceramide synthase inhibition by fumonisin B 1. Structure (2024)

Release Date

2024-11-27

Peptides

Ceramide synthase LAC1: AC
Ceramide synthase subunit LIP1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane

We predict this structure to be a membrane protein.
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Ceramide synthase LAC1

Ceramide synthase subunit LIP1

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