SMTL ID : 7k0m.1

Human serine palmitoyltransferase complex SPTLC1/SPLTC2/ssSPTa/ORMDL3, class 1

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 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.263, B:A.346, B:K.379 Hydrogen bonds: B:G.238, B:F.239, B:S.265, B:K.379, A:A.339 Salt bridges: B:K.379 pi-Stacking: B:H.263 PLP.16: 13 residues within 4Å: Chain G: 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 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:H.263, H:A.346, H:K.379 Hydrogen bonds: H:G.238, H:F.239, H:S.265, H:K.379, G:A.339 Salt bridges: H:K.379 pi-Stacking: H:H.263

14 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, F.84, Y.86, L.87, F.90, Y.93 Chain C: M.40 Ligands: POV.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.83, B:Y.93 POV.3: 6 residues within 4Å: Chain B: Y.122 Chain D: N.13, G.69, P.71, H.85 Ligands: POV.8 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.71 POV.4: 1 residues within 4Å: Ligands: POV.2 No protein-ligand interaction detected (PLIP) POV.5: 3 residues within 4Å: Chain C: T.35, S.39, M.40 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.35 POV.6: 1 residues within 4Å: Chain C: N.38 No protein-ligand interaction detected (PLIP) POV.7: 5 residues within 4Å: Chain D: I.30, F.101, I.104, T.105, L.109 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.30, D:F.101, D:I.104, D:L.109 POV.8: 6 residues within 4Å: Chain B: V.76 Chain D: I.22, S.25, Y.26, A.29 Ligands: POV.3 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:I.22, D:Y.26, D:A.29, B:V.76 POV.9: 1 residues within 4Å: Ligands: POV.14 No protein-ligand interaction detected (PLIP) POV.10: 3 residues within 4Å: Chain E: T.35, S.39, M.40 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.35 POV.11: 1 residues within 4Å: Chain E: N.38 No protein-ligand interaction detected (PLIP) POV.12: 5 residues within 4Å: Chain F: I.30, F.101, I.104, T.105, L.109 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:I.30, F:F.101, F:I.104, F:L.109 POV.13: 7 residues within 4Å: Chain F: I.22, S.25, Y.26, A.29 Chain H: Y.75, V.76 Ligands: POV.15 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: F:I.22, F:Y.26, F:A.29, H:V.76 POV.14: 9 residues within 4Å: Chain E: M.40 Chain F: I.62, V.67 Chain H: L.83, F.84, Y.86, L.87, F.90 Ligands: POV.9 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain H Hydrophobic interactions: F:I.62, F:V.67, H:L.83 POV.15: 6 residues within 4Å: Chain F: N.13, G.69, P.71, H.85 Chain H: Y.122 Ligands: POV.13 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.71

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: AG
Serine palmitoyltransferase 2: BH
Serine palmitoyltransferase small subunit A: CE
ORM1-like protein 3: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
E

B
B

H
F

C
C

E
G

D
D

F
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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