SMTL ID : 7pax.1

Structure of the human heterotetrameric cis-prenyltransferase complex in complex with magnesium, FsPP and IPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.1: 17 residues within 4Å: Chain A: I.39, D.41, Y.83, A.84, F.85, S.86, N.89, R.92, R.212, R.218, S.220 Chain B: L.186, R.216, L.217, G.218 Ligands: FPS.2, MG.3 20 PLIP interactions: 13 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.39, A:Y.83, A:Y.83, A:Y.83 Hydrogen bonds: A:N.89, A:N.89, A:R.92, A:S.220, A:S.220, B:L.217, B:G.218 Water bridges: A:R.212, B:R.216, B:R.216, B:R.216, B:R.216, B:R.216 Salt bridges: A:R.212, A:R.212, A:R.218 IPE.4: 17 residues within 4Å: Chain C: I.39, D.41, Y.83, A.84, F.85, S.86, N.89, R.92, R.212, R.218, S.220 Chain D: L.186, R.216, L.217, G.218 Ligands: FPS.5, MG.6 20 PLIP interactions: 13 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:I.39, C:Y.83, C:Y.83, C:Y.83 Hydrogen bonds: C:N.89, C:N.89, C:R.92, C:S.220, C:S.220, D:L.217, D:G.218 Water bridges: C:R.212, D:R.216, D:R.216, D:R.216, D:R.216, D:R.216 Salt bridges: C:R.212, C:R.212, C:R.218

2 x FPS: S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE(Non-covalent)

FPS.2: 19 residues within 4Å: Chain A: W.10, M.40, D.41, G.42, N.43, R.44, R.45, H.58, F.62, A.84, N.89, R.92, L.100, L.103, K.107, V.159, F.161 Ligands: IPE.1, MG.3 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.10, A:F.62, A:F.62, A:A.84, A:L.100, A:L.103, A:K.107, A:V.159 Hydrogen bonds: A:G.42, A:R.44, A:R.45, A:R.92, A:R.92 Water bridges: A:D.41, A:R.44, A:R.44, A:R.44, B:R.216 Salt bridges: A:R.44, A:R.45, B:R.216 FPS.5: 19 residues within 4Å: Chain C: W.10, M.40, D.41, G.42, N.43, R.44, R.45, H.58, F.62, A.84, N.89, R.92, L.100, L.103, K.107, V.159, F.161 Ligands: IPE.4, MG.6 21 PLIP interactions: 19 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.10, C:F.62, C:F.62, C:A.84, C:L.100, C:L.103, C:K.107, C:V.159 Hydrogen bonds: C:G.42, C:R.44, C:R.45, C:R.92, C:R.92 Water bridges: C:D.41, C:R.44, C:R.44, C:R.44, D:R.216 Salt bridges: C:R.44, C:R.45, D:R.216

2 x MG: MAGNESIUM ION(Non-covalent)

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

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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