SMTL ID : 5hc7.1

Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with S-thiolo-isopentenyldiphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.21, R.72 Ligands: DST.2, DST.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.21, H2O.1 MG.4: 4 residues within 4Å: Chain B: D.21, R.72 Ligands: DST.5, DST.6 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.21, H2O.4

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

DST.2: 13 residues within 4Å: Chain A: I.20, D.21, W.63, A.64, L.65, S.66, N.69, R.72, R.193, R.199, S.201 Ligands: MG.1, DST.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.20, A:W.63, A:W.63 Hydrogen bonds: A:N.69, A:R.72, A:S.201 Water bridges: A:R.72, A:R.193, A:R.199 Salt bridges: A:R.193, A:R.199 DST.3: 9 residues within 4Å: Chain A: D.21, G.22, H.23, R.24, K.25, H.38, R.72 Ligands: MG.1, DST.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.21, A:G.22, A:H.23, A:H.23, A:R.24, A:K.25, A:R.72, A:R.72 Water bridges: A:R.24 Salt bridges: A:R.24, A:K.25 DST.5: 13 residues within 4Å: Chain B: I.20, D.21, W.63, A.64, L.65, S.66, N.69, R.72, R.193, R.199, S.201 Ligands: MG.4, DST.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.20, B:W.63, B:W.63 Hydrogen bonds: B:N.69, B:R.72, B:S.201 Water bridges: B:R.72, B:R.193, B:R.199 Salt bridges: B:R.193, B:R.199 DST.6: 9 residues within 4Å: Chain B: D.21, G.22, H.23, R.24, K.25, H.38, R.72 Ligands: MG.4, DST.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.22, B:H.23, B:H.23, B:R.24, B:K.25, B:R.72, B:R.72 Water bridges: B:R.24 Salt bridges: B:R.24, B:K.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, M.X. et al., Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-03-02

Peptides

prenyltransference for protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

prenyltransference for protein

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