SMTL ID : 7yiy.1

Cryo-EM structure of SPT-ORMDL3 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: G.238, F.239, N.242, H.263, S.265, D.344, A.346, H.347, T.376, T.378, K.379 Chain E: S.288, A.289 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:H.263 Hydrogen bonds: A:G.238, A:F.239, A:N.242, A:S.265, A:T.378, A:K.379, E:A.289 Salt bridges: A:K.379 pi-Stacking: A:H.263

1 x Z1T: N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide(Non-covalent)

Z1T.2: 12 residues within 4Å: Chain A: Y.75, V.76, L.83, Y.122 Chain C: N.13, V.16, S.25, L.28, F.63, G.69, P.71, H.85 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:V.16, C:L.28, C:F.63, A:Y.75, A:L.83 Hydrogen bonds: C:N.13, C:N.13, C:F.63, C:G.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis. Nat Commun (2023)

Release Date

2023-07-05

Peptides

Serine palmitoyltransferase 2: A
Serine palmitoyltransferase 1: B
ORM1-like protein 3: C
Serine palmitoyltransferase small subunit A: D
Serine palmitoyltransferase 1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
D

D
C

E
A

Membrane

We predict this structure to be a membrane protein.
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Serine palmitoyltransferase 2

Serine palmitoyltransferase 1

ORM1-like protein 3

Serine palmitoyltransferase small subunit A

Serine palmitoyltransferase 1

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