SMTL ID : 8iak.1

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3A-N71A) complex

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.361, A.362 Chain B: Y.226, N.229, H.250, S.252, E.302, D.331, A.333, H.334, T.363, T.365, K.366 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.250, B:E.302, B:K.366 Hydrogen bonds: B:Y.226, B:N.229, B:E.302, B:T.363, B:T.365, B:T.365, A:A.362 Salt bridges: B:K.366 pi-Stacking: B:H.250 PLP.2: 13 residues within 4Å: Chain E: S.361, A.362 Chain F: Y.226, N.229, H.250, S.252, E.302, D.331, A.333, H.334, T.363, T.365, K.366 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:H.250, F:E.302, F:K.366 Hydrogen bonds: F:Y.226, F:N.229, F:E.302, F:T.363, F:T.365, F:T.365, E:A.362 Salt bridges: F:K.366 pi-Stacking: F:H.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, T. et al., Collaborative regulation of yeast SPT-Orm2 complex by phosphorylation and ceramide. Cell Rep (2024)

Release Date

2024-02-14

Peptides

chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1: AE
Serine palmitoyltransferase 2: BF
Protein ORM2: CG
Serine palmitoyltransferase-regulating protein TSC3: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
D

G
H

D
C

H
G

Membrane

We predict this structure to be a membrane protein.
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chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1

Serine palmitoyltransferase 2

Protein ORM2

Serine palmitoyltransferase-regulating protein TSC3

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