SMTL ID : 8x36.1

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form B)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

2 x DST: DIMETHYLALLYL S-THIOLODIPHOSPHATE(Non-covalent)

DST.1: 12 residues within 4Å: Chain A: M.44, D.45, G.46, N.47, R.48, R.49, H.62, I.65, A.88, R.96 Ligands: IPE.2, MG.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.65 Hydrogen bonds: A:G.46, A:N.47, A:R.48, A:R.49, A:R.96, A:R.96 Water bridges: A:R.48, A:R.48, B:R.256 Salt bridges: A:R.48, A:R.49 DST.6: 12 residues within 4Å: Chain B: M.44, D.45, G.46, N.47, R.48, R.49, H.62, A.88, N.93, R.96 Ligands: IPE.4, MG.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.46, B:N.47, B:R.48, B:R.48, B:R.48, B:R.49, B:R.96, B:R.96 Salt bridges: B:R.48, B:R.49

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

IPE.2: 18 residues within 4Å: Chain A: I.43, M.44, D.45, F.87, A.88, F.89, S.90, N.93, R.96, R.208, R.214, S.216 Chain B: Y.225, R.256, F.257, G.258 Ligands: DST.1, MG.3 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.43, A:F.87 Hydrogen bonds: A:N.93, A:S.216, B:G.258 Water bridges: A:R.96, A:R.96, A:R.208, B:R.256, B:R.256, B:F.257, B:G.258 Salt bridges: A:R.96, A:R.208, A:R.208, A:R.214 IPE.4: 10 residues within 4Å: Chain B: D.45, R.48, E.92, R.96, R.208, E.212, R.214, S.216 Ligands: MG.5, DST.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.208, B:S.216, B:S.216 Water bridges: B:R.96, B:R.96 Salt bridges: B:R.96, B:R.208, B:R.214

2 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imaizumi, R. et al., Structural-Functional Correlations between Unique N-terminal Region and C-terminal Conserved Motif in Short-chain cis-Prenyltransferase from Tomato. Chembiochem (2024)

Release Date

2024-02-07

Peptides

Neryl-diphosphate synthase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neryl-diphosphate synthase 1

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