SMTL ID : 7pay.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-mer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: R.212, R.218, S.220 Chain B: L.186, R.216, L.217, G.218 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.220, B:R.216, B:L.217, B:G.218 Water bridges: A:R.212, A:R.212, A:R.212, A:R.218, A:R.218, B:G.218, B:K.219 Salt bridges: A:R.212, A:R.218 SO4.4: 7 residues within 4Å: Chain C: R.212, R.218, S.220 Chain D: L.186, R.216, L.217, G.218 12 PLIP interactions: 4 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:R.216, D:L.217, D:G.218, C:S.220 Water bridges: D:G.218, C:R.212, C:R.212, C:R.212, C:R.218, C:R.218 Salt bridges: C:R.212, C:R.218

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

GGS.3: 17 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, K.107, F.161 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.62, A:L.65, A:A.104, A:K.107, A:F.161 Hydrogen bonds: A:G.42, A:R.44, A:R.45, A:R.92, A:R.92 Water bridges: A:R.44, A:R.44, A:R.44, A:R.212 Salt bridges: A:R.44, A:R.45 GGS.6: 17 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, K.107, F.161 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.62, C:L.65, C:A.104, C:K.107, C:F.161 Hydrogen bonds: C:D.41, C:G.42, C:R.44, C:R.45, C:R.92, C:R.92 Water bridges: C:R.44, C:R.44, C:R.44, C:R.212 Salt bridges: C:R.44, C:R.45

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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