SMTL ID : 7vpc.1 (1 other biounit)

Neryl diphosphate synthase from Solanum lycopersicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: R.96 Ligands: MLT.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 EDO.3: 5 residues within 4Å: Chain A: D.45, G.46, N.47, R.48, R.49 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.46, A:N.47, A:N.47, A:R.48, A:R.49 EDO.4: 7 residues within 4Å: Chain A: Y.229, T.231, T.233, F.238, D.242, E.245, A.246 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.229, A:T.231, A:T.233, A:T.233, A:D.242, A:D.242, A:A.246 EDO.5: 6 residues within 4Å: Chain A: I.125, V.155, E.197, S.198, K.199 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.199 EDO.6: 8 residues within 4Å: Chain A: H.39, I.83, T.85, V.155, S.198, K.199, P.201 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.198

1 x MLT: D-MALATE(Non-covalent)

MLT.2: 7 residues within 4Å: Chain A: I.43, M.44, D.45, F.87, R.208, S.216 Ligands: EDO.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.87 Hydrogen bonds: A:M.44, A:D.45, A:S.216 Water bridges: A:R.208 Salt bridges: A:R.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kutsukawa, R. et al., Structure-based engineering of a short-chain cis-prenyltransferase to biosynthesize nonnatural all-cis-polyisoprenoids: molecular mechanisms for primer substrate recognition and ultimate product chain-length determination. Febs J. (2022)

Release Date

2022-05-18

Peptides

Neryl-diphosphate synthase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Neryl-diphosphate synthase 1

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