SMTL ID : 6z1n.1

Structure of the human heterotetrameric cis-prenyltransferase complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.1: 21 residues within 4Å: Chain A: W.10, M.40, D.41, G.42, N.43, R.44, R.45, H.58, G.61, F.62, A.84, N.89, R.92, L.100, L.103, A.104, K.107, F.108, V.159, F.161 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.10, A:F.62, A:F.62, A:A.84, A:L.100, A:L.103, A:K.107, A:F.108, A:V.159 Hydrogen bonds: A:G.42, A:N.43, A:R.44, A:R.45 Water bridges: A:R.44, A:R.44, A:R.45 Salt bridges: A:R.44, A:R.44, A:R.45, A:H.58, A:R.92 FPP.4: 21 residues within 4Å: Chain C: W.10, M.40, D.41, G.42, N.43, R.44, R.45, H.58, G.61, F.62, A.84, N.89, R.92, L.100, L.103, A.104, K.107, F.108, V.159, F.161 Ligands: MG.6 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:W.10, C:F.62, C:F.62, C:A.84, C:L.100, C:L.103, C:K.107, C:F.108, C:V.159 Hydrogen bonds: C:D.41, C:G.42, C:N.43, C:R.44, C:R.45 Water bridges: C:R.44, C:R.44, C:R.45 Salt bridges: C:R.44, C:R.44, C:R.45, C:H.58, C:R.92

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: R.212, R.218, S.220 Chain B: R.216, L.217, G.218 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.216, B:L.217, B:G.218, A:S.220 Water bridges: B:G.218, B:K.219, A:R.212, A:R.212, A:R.212, A:R.218, A:R.218, A:R.218, A:R.218 Salt bridges: A:R.212, A:R.218 PO4.5: 6 residues within 4Å: Chain C: R.212, R.218, S.220 Chain D: R.216, L.217, G.218 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.220, D:R.216, D:L.217, D:G.218 Water bridges: C:R.212, C:R.212, C:R.212, C:R.218, C:R.218, C:R.218, C:R.218, D:G.218 Salt bridges: C:R.212, C:R.218

2 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bar-El, M.L. et al., Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex. Nat Commun (2020)

Release Date

2020-10-21

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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