SMTL ID : 7pb1.1

Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, GGPP and IsPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.41, R.45 Ligands: GRG.2, ISY.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.41, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain C: D.41, R.45 Ligands: GRG.5, ISY.6 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.41, H2O.1, H2O.1

2 x GRG: GERANYLGERANYL DIPHOSPHATE(Non-covalent)

GRG.2: 21 residues within 4Å: Chain A: M.40, D.41, G.42, N.43, R.44, R.45, H.58, F.62, L.65, A.84, N.89, R.92, L.103, A.104, F.108, L.111, I.125, V.159, F.161 Ligands: MG.1, ISY.3 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.62, A:F.62, A:L.65, A:L.103, A:A.104, A:F.108, A:L.111, A:I.125, A:V.159, A:F.161 Hydrogen bonds: A:G.42, A:N.43, A:R.44, A:R.45 Water bridges: A:R.44, A:R.44, B:R.216 Salt bridges: A:R.44, A:R.44, A:R.45, A:H.58, A:R.92, B:R.216 GRG.5: 21 residues within 4Å: Chain C: M.40, D.41, G.42, N.43, R.44, R.45, H.58, F.62, L.65, A.84, N.89, R.92, L.103, A.104, F.108, L.111, I.125, V.159, F.161 Ligands: MG.4, ISY.6 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.62, C:F.62, C:L.65, C:L.103, C:A.104, C:F.108, C:L.111, C:I.125, C:V.159, C:F.161 Hydrogen bonds: C:G.42, C:N.43, C:R.44, C:R.45 Water bridges: C:R.44, C:R.44, D:R.216 Salt bridges: C:R.44, C:R.44, C:R.45, C:H.58, C:R.92, D:R.216

2 x ISY: 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid(Non-covalent)

ISY.3: 17 residues within 4Å: Chain A: I.39, M.40, D.41, Y.83, A.84, F.85, S.86, N.89, R.92, R.212, R.218, S.220 Chain B: R.216, L.217, G.218 Ligands: MG.1, GRG.2 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:R.216, B:L.217, B:G.218, A:N.89, A:R.92, A:S.220, A:S.220 Water bridges: B:R.216, B:R.216, A:R.212, A:R.212 Salt bridges: B:R.216, A:R.212, A:R.218 Hydrophobic interactions: A:I.39, A:Y.83, A:Y.83 ISY.6: 17 residues within 4Å: Chain C: I.39, M.40, D.41, Y.83, A.84, F.85, S.86, N.89, R.92, R.212, R.218, S.220 Chain D: R.216, L.217, G.218 Ligands: MG.4, GRG.5 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.39, C:Y.83, C:Y.83 Hydrogen bonds: C:N.89, C:R.92, C:S.220, C:S.220, D:R.216, D:L.217, D:G.218 Water bridges: C:R.212, C:R.212, D:R.216, D:R.216 Salt bridges: C:R.212, C:R.218, D:R.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giladi, M. et al., Structural basis for long-chain isoprenoid synthesis by cis -prenyltransferases. Sci Adv (2022)

Release Date

2022-06-01

Peptides

Dehydrodolichyl diphosphate synthase complex subunit DHDDS: AC
Dehydrodolichyl diphosphate synthase complex subunit NUS1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Dehydrodolichyl diphosphate synthase complex subunit DHDDS

Dehydrodolichyl diphosphate synthase complex subunit NUS1

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