SMTL ID : 7k0o.1

Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: S.338, A.339 Chain B: G.238, F.239, H.263, S.265, E.315, D.344, A.346, H.347, T.376, T.378, K.379 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.346, B:K.379 Hydrogen bonds: B:G.238, B:F.239, B:S.265, B:T.376, B:T.378, B:T.378, A:S.338, A:A.339 Salt bridges: B:K.379 pi-Stacking: B:H.263 PLP.14: 13 residues within 4Å: Chain E: S.338, A.339 Chain H: G.238, F.239, H.263, S.265, E.315, D.344, A.346, H.347, T.376, T.378, K.379 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain E Hydrophobic interactions: H:A.346, H:K.379 Hydrogen bonds: H:G.238, H:F.239, H:S.265, H:T.376, H:T.378, H:T.378, E:S.338, E:A.339 Salt bridges: H:K.379 pi-Stacking: H:H.263

12 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)(Non-functional Binders)

POV.2: 8 residues within 4Å: Chain B: L.83, Y.86, L.87, F.90 Chain C: M.40 Chain D: I.62, V.67 Ligands: POV.4 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.62, D:V.67, B:L.83, B:F.90 POV.3: 7 residues within 4Å: Chain B: G.79, Y.122 Chain D: N.13, G.69, P.71, H.85 Ligands: POV.7 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.71 POV.4: 2 residues within 4Å: Ligands: POV.2, POV.5 No protein-ligand interaction detected (PLIP) POV.5: 2 residues within 4Å: Chain C: S.39 Ligands: POV.4 No protein-ligand interaction detected (PLIP) POV.6: 1 residues within 4Å: Chain D: T.105 No protein-ligand interaction detected (PLIP) POV.7: 6 residues within 4Å: Chain B: Y.75, V.76 Chain D: M.17, I.22, S.25 Ligands: POV.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.76, D:I.22 POV.8: 2 residues within 4Å: Ligands: POV.9, POV.13 No protein-ligand interaction detected (PLIP) POV.9: 2 residues within 4Å: Chain F: S.39 Ligands: POV.8 No protein-ligand interaction detected (PLIP) POV.10: 1 residues within 4Å: Chain G: T.105 No protein-ligand interaction detected (PLIP) POV.11: 6 residues within 4Å: Chain G: M.17, I.22, S.25 Chain H: Y.75, V.76 Ligands: POV.12 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:I.22, H:V.76 POV.12: 7 residues within 4Å: Chain G: N.13, G.69, P.71, H.85 Chain H: G.79, Y.122 Ligands: POV.11 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:P.71 POV.13: 8 residues within 4Å: Chain F: M.40 Chain G: I.62, V.67 Chain H: L.83, Y.86, L.87, F.90 Ligands: POV.8 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:L.83, G:I.62, G:V.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Structural insights into the regulation of human serine palmitoyltransferase complexes. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-02-24

Peptides

Serine palmitoyltransferase 1: AE
Serine palmitoyltransferase 2: BH
Serine palmitoyltransferase small subunit A: CF
ORM1-like protein 3: DG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

H
F

C
C

F
G

D
D

G
H

Membrane

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

Serine palmitoyltransferase 2

Serine palmitoyltransferase small subunit A

ORM1-like protein 3

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