SMTL ID : 8y2m.1

Cryo-EM structure of the 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: 11 residues within 4Å: Chain A: V.114, A.115, F.135, Y.139, Y.182, S.186, F.218, V.222, G.226, Q.227, F.230 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.115, A:F.135, A:F.135, A:Y.139, A:Y.182, A:F.218, A:F.218, A:F.230, A:F.230 6PL.4: 10 residues within 4Å: Chain B: A.36, Y.39, F.40, N.47, F.51, K.86, R.90 Chain D: Y.39 Ligands: 7PO.3, 6PL.9 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.39, B:Y.39, B:F.40, B:F.40, B:F.40, B:F.40 Hydrogen bonds: B:N.47 Salt bridges: B:K.86, B:R.90 6PL.5: 13 residues within 4Å: Chain A: K.128, G.129, D.132, L.133, V.136, A.228, L.260, L.261, W.264, V.268 Chain B: I.34, E.38, K.41 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.128, A:D.132, A:L.133, A:L.133, A:V.136, A:A.228, A:L.261, A:W.264, A:V.268, B:I.34 6PL.6: 11 residues within 4Å: Chain C: V.114, A.115, F.135, Y.139, Y.182, S.186, F.218, V.222, G.226, Q.227, F.230 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.115, C:F.135, C:F.135, C:Y.139, C:Y.182, C:F.218, C:F.218, C:F.230, C:F.230 6PL.9: 10 residues within 4Å: Chain B: Y.39 Chain D: A.36, Y.39, F.40, N.47, F.51, K.86, R.90 Ligands: 6PL.4, 7PO.8 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.39, D:Y.39, D:F.40, D:F.40, D:F.40, D:F.40 Hydrogen bonds: D:N.47 Salt bridges: D:K.86, D:R.90 6PL.10: 13 residues within 4Å: Chain C: K.128, G.129, D.132, L.133, V.136, A.228, L.260, L.261, W.264, V.268 Chain D: I.34, E.38, K.41 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:K.128, C:D.132, C:L.133, C:L.133, C:V.136, C:A.228, C:L.261, C:W.264, C:V.268, D:I.34

2 x 01: (2~{R})-2-[2-[(5~{R},6~{R},7~{S},9~{S},11~{R},16~{R},18~{S},19~{S})-19-azanyl-6-[(3~{R})-3-carboxy-5-oxidanyl-5-oxidanylidene-pentanoyl]oxy-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid

01.2: 17 residues within 4Å: Chain A: R.172, Y.182, W.231, H.255, D.286, L.289, K.293, N.296, Y.297, A.303, F.304, F.307, W.371, I.375, V.378, I.382, R.385 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.293, A:N.296, A:A.303, A:F.307, A:W.371, A:I.375, A:V.378 Hydrogen bonds: A:H.255, A:N.296 Salt bridges: A:R.172, A:R.385 01.7: 17 residues within 4Å: Chain C: R.172, Y.182, W.231, H.255, D.286, L.289, K.293, N.296, Y.297, A.303, F.304, F.307, W.371, I.375, V.378, I.382, R.385 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:K.293, C:N.296, C:A.303, C:F.307, C:W.371, C:I.375, C:V.378 Hydrogen bonds: C:H.255, C:N.296 Salt bridges: C:R.172, C:R.385

2 x 7PO: hexacosanoic acid(Non-covalent)

7PO.3: 21 residues within 4Å: Chain A: Y.224, W.231, H.255, L.262, S.265, S.266, F.269, F.271, M.274, G.275, Y.279, M.282, D.283, D.286, Y.348, I.352, S.353, I.356, V.357, L.360 Ligands: 6PL.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.231, A:L.262, A:L.262, A:F.269, A:F.269, A:F.269, A:Y.279, A:Y.279, A:M.282, A:I.352, A:I.356, A:I.356, A:L.360 7PO.8: 21 residues within 4Å: Chain C: Y.224, W.231, H.255, L.262, S.265, S.266, F.269, F.271, M.274, G.275, Y.279, M.282, D.283, D.286, Y.348, I.352, S.353, I.356, V.357, L.360 Ligands: 6PL.9 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.231, C:L.262, C:L.262, C:F.269, C:F.269, C:F.269, C:Y.279, C:Y.279, C:M.282, C:I.352, C:I.356, C:I.356, C:L.360

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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