SMTL ID : 7cqk.1

Cryo-EM structure of the substrate-bound SPT-ORMDL3 complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-mer

Ligands

1 x PLS: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE(Non-covalent)

PLS.1: 17 residues within 4Å: Chain A: P.135, F.337, S.338, A.339 Chain B: Y.176, G.238, F.239, N.242, H.263, S.265, E.315, D.344, H.347, M.374, T.376, K.379 Ligands: GE0.2 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.176, B:Y.176, B:G.238, B:F.239, B:H.263, B:S.265, B:T.378, B:K.379, B:K.379, A:A.339 Salt bridges: B:H.263, B:K.379 pi-Stacking: B:H.263

1 x GE0: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-[2-(2-oxidanylideneheptadecylsulfanyl)ethylamino]propyl]amino]butyl] hydrogen phosphate(Covalent)

GE0.2: 25 residues within 4Å: Chain A: P.135, F.138, R.203, C.336, F.337 Chain B: Y.122, Y.127, W.134, Y.176, S.258, D.259, E.260, N.262, H.263, V.267, R.271, I.277, I.279, M.320, G.497, P.499 Chain C: P.75, D.76, Y.91 Ligands: PLS.1 18 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: B:Y.127, B:W.134, B:P.499, A:P.135, A:F.138, A:F.138, A:F.138 Hydrogen bonds: B:S.258, B:D.259, B:A.264, B:S.319, C:P.75, C:D.76, C:D.76, C:Y.91, C:Y.91 Salt bridges: B:R.271, A:R.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-02-10

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

E
C

B
T

C
A

D
E

Membrane

We predict this structure to be a membrane protein.
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Serine palmitoyltransferase 1

Serine palmitoyltransferase 2

ORM1-like protein 3

Serine palmitoyltransferase small subunit A

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