SMTL ID : 6j7f.1

Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 7 residues within 4Å: Chain B: L.254, K.255, G.258, R.259, L.260, H.261, V.335 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.255, B:L.260, B:H.261, B:V.335 Salt bridges: B:K.255, B:K.255, B:H.261

1 x FAR: FARNESYL(Covalent)

FAR.2: 10 residues within 4Å: Chain B: I.32, Y.35, S.47, R.51, G.54, I.55, W.57, P.293, F.294 Chain C: C.195 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.35, B:P.293

1 x GER: GERAN-8-YL GERAN(Covalent)

GER.3: 16 residues within 4Å: Chain B: L.101, Q.108, R.149, F.152, G.197, Q.198, Y.200, C.201, Y.246, W.248, W.249, F.298, C.319 Chain C: C.194, C.195 Ligands: DPO.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.101, B:W.249, B:F.298

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.4: 10 residues within 4Å: Chain A: K.135, Y.191, S.193, Y.195 Chain B: H.195, R.237, K.240, Y.246 Chain C: C.194 Ligands: GER.3 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.246, A:Y.195 Salt bridges: B:H.195, B:R.237, B:K.240, B:K.240, A:K.135, A:K.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto-Ito, S. et al., Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP. To Be Published

Release Date

2020-01-22

Peptides

Protein prenyltransferase alpha subunit repeat-containing protein 1: A
Geranylgeranyl transferase type-2 subunit beta: B
Synaptobrevin homolog YKT6: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Protein prenyltransferase alpha subunit repeat-containing protein 1

Geranylgeranyl transferase type-2 subunit beta

Synaptobrevin homolog YKT6

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