SMTL ID : 8hf3.1

Cryo-EM structure of human ZDHHC9/GCP16 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.141, C.144, H.154, C.161 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.141, A:C.144, A:H.154, A:C.161 ZN.2: 4 residues within 4Å: Chain A: C.155, C.158, H.168, C.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.155, A:C.158, A:H.168, A:C.175

4 x PLM: PALMITIC ACID(Covalent)

PLM.3: 10 residues within 4Å: Chain A: L.44, I.45, T.48, H.167, C.169, W.171, L.191, T.195, T.235, L.242 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.44, A:I.45, A:T.48, A:W.171, A:T.235, A:L.242 PLM.4: 4 residues within 4Å: Chain A: C.25, F.88 Ligands: PLM.5, PX2.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.88 PLM.5: 11 residues within 4Å: Chain A: C.24, M.31, K.35, F.38, Y.39, L.42, M.80, L.84, F.88 Ligands: PLM.4, PX2.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.38, A:Y.39, A:L.42, A:L.84, A:F.88 PLM.6: 10 residues within 4Å: Chain A: F.71, L.75, F.78, L.186, L.193, L.287, C.288 Chain B: G.75, C.76, C.79 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.71, A:L.75, A:F.78, A:L.186, A:L.193, A:L.287

1 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.7: 15 residues within 4Å: Chain A: R.28, F.76, L.77, M.80, L.84, R.85, F.88, S.89, D.90, R.179, R.298 Chain B: T.84, L.87 Ligands: PLM.4, PLM.5 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.76, A:M.80, A:L.84, B:T.84 Hydrogen bonds: A:D.90 Salt bridges: A:R.85, A:R.179, A:R.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, A. et al., Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-11-22

Peptides

Palmitoyltransferase ZDHHC9: A
Golgin subfamily A member 7: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Palmitoyltransferase ZDHHC9

Golgin subfamily A member 7