SMTL ID : 9r0e.1

Structure of the human heterotetrameric cis-prenyltransferase complex harboring NgBR-S249T in complex with magnesium, FsPP and IPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

hetero-2-2-mer

Ligands

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

IPE.1: 16 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: R.210, L.211, G.212 Ligands: FPS.2, MG.3 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.210, B:L.211, B:G.212, A:N.89, A:S.220 Hydrophobic interactions: A:I.39, A:Y.83, A:Y.83, A:Y.83 Salt bridges: A:R.92, A:R.212, A:R.212, A:R.218 IPE.4: 16 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: R.210, L.211, G.212 Ligands: FPS.5, MG.6 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.39, C:Y.83, C:Y.83, C:Y.83 Hydrogen bonds: C:N.89, C:S.220, D:R.210, D:L.211, D:G.212 Salt bridges: C:R.92, 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 19 PLIP interactions: 1 interactions with chain B, 18 interactions with chain A Salt bridges: B:R.210, A:R.44, A:R.45 Hydrophobic interactions: A:W.10, A:F.62, A:F.62, A:F.62, A:L.100, A:L.100, A:L.103, A:K.107, A:V.159 Hydrogen bonds: A:D.41, A:G.42, A:N.43, A:R.44, A:R.45, A:R.92, A:R.92 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 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.10, C:F.62, C:F.62, C:F.62, C:L.100, C:L.100, C:L.103, C:K.107, C:V.159 Hydrogen bonds: C:D.41, C:G.42, C:N.43, C:R.44, C:R.45, C:R.92, C:R.92 Salt bridges: C:R.44, C:R.45, D:R.210

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.41, R.45 Chain B: R.210 Ligands: IPE.1, FPS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.41 MG.6: 5 residues within 4Å: Chain C: D.41, R.45 Chain D: R.210 Ligands: IPE.4, FPS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giladi, M. et al., Structural mechanisms of allosteric network regulation in the human cis-prenyltransferase complex. To Be Published

Release Date

2025-10-29

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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