SMTL ID : 7pb0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

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

ISY.1: 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: GGS.2, MG.3 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.39, A:Y.83, A:Y.83, A:Y.83 Hydrogen bonds: A:N.89, A:R.92, A:R.212, A:S.220, B:L.217, B:G.218 Water bridges: A:R.44, A:S.220, B:R.216, B:R.216, B:R.216, B:G.218 Salt bridges: A:R.212, A:R.218 ISY.4: 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: GGS.5, MG.6 18 PLIP interactions: 12 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:I.39, C:Y.83, C:Y.83, C:Y.83 Hydrogen bonds: C:N.89, C:R.92, C:R.212, C:S.220, D:L.217, D:G.218 Water bridges: C:R.44, C:S.220, D:R.216, D:R.216, D:R.216, D:G.218 Salt bridges: C:R.212, C:R.218

2 x GGS: phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid(Non-covalent)

GGS.2: 18 residues within 4Å: Chain A: M.40, D.41, G.42, N.43, R.44, R.45, H.58, G.61, F.62, L.65, A.84, R.92, L.100, A.104, V.159, F.161 Ligands: ISY.1, MG.3 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.65, A:A.84, A:L.100, A:A.104, A:V.159, A:F.161 Hydrogen bonds: A:G.42, A:N.43, A:R.44, A:R.45, A:R.92, A:R.92 Water bridges: A:R.44, B:R.216, B:R.216 Salt bridges: A:R.44, A:R.45 GGS.5: 18 residues within 4Å: Chain C: M.40, D.41, G.42, N.43, R.44, R.45, H.58, G.61, F.62, L.65, A.84, R.92, L.100, A.104, V.159, F.161 Ligands: ISY.4, MG.6 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.65, C:A.84, C:L.100, C:A.104, C:V.159, C:F.161 Hydrogen bonds: C:G.42, C:N.43, C:R.44, C:R.45, C:R.92, C:R.92 Water bridges: C:R.44, D:R.216, D:R.216 Salt bridges: C:R.44, C:R.45

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.41, R.45 Ligands: ISY.1, GGS.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.41, H2O.1, H2O.2 MG.6: 4 residues within 4Å: Chain C: D.41, R.45 Ligands: ISY.4, GGS.5 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.41, H2O.6, H2O.7

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

Related Entries With Identical Sequence