SMTL ID : 5hc8.1

Crystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with dimethylallyl diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.21 Ligands: PIS.2, ISY.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.21, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: D.21 Ligands: PIS.7, ISY.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.21, H2O.6, H2O.6

2 x PIS: TRIHYDROGEN THIODIPHOSPHATE(Non-covalent)

PIS.2: 10 residues within 4Å: Chain A: D.21, G.22, H.23, R.24, K.25, H.38, R.72 Ligands: MG.1, 61G.3, ISY.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.21, A:D.21, A:D.21, A:G.22, A:G.22, A:H.23, A:R.24, A:R.24, A:K.25, A:R.72, A:R.72 Salt bridges: A:R.24 PIS.7: 10 residues within 4Å: Chain B: D.21, G.22, H.23, R.24, K.25, H.38, R.72 Ligands: MG.6, 61G.8, ISY.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.21, B:D.21, B:G.22, 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

2 x 61G: 2-methylbuta-1,3-diene(Non-covalent)

61G.3: 10 residues within 4Å: Chain A: I.20, H.23, H.38, A.64, N.69, R.72, L.80, Y.84 Ligands: PIS.2, ISY.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.20, A:L.80 61G.8: 10 residues within 4Å: Chain B: I.20, H.23, H.38, A.64, N.69, R.72, L.80, Y.84 Ligands: PIS.7, ISY.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.20, B:L.80

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: H.135, T.183, K.184, F.185 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.184 Water bridges: A:H.135, A:H.135 Salt bridges: A:H.135, A:K.184 SO4.9: 4 residues within 4Å: Chain B: H.135, T.183, K.184, F.185 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.184 Water bridges: B:H.135, B:H.135 Salt bridges: B:H.135, B:K.184

2 x ISY: 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid(Non-covalent)

ISY.5: 17 residues within 4Å: Chain A: I.19, I.20, D.21, W.63, A.64, S.66, N.69, R.72, R.193, R.199, S.201 Chain B: G.241, F.242, G.243 Ligands: MG.1, PIS.2, 61G.3 21 PLIP interactions: 4 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:G.241, B:F.242, B:G.243, B:G.243, A:N.69, A:R.72, A:S.201, A:S.201 Hydrophobic interactions: A:I.19, A:I.20, A:W.63, A:W.63, A:W.63, A:W.63 Water bridges: A:D.21, A:D.21, A:R.193, A:R.199, A:R.199 Salt bridges: A:R.193, A:R.199 ISY.10: 17 residues within 4Å: Chain A: G.241, F.242, G.243 Chain B: I.19, I.20, D.21, W.63, A.64, S.66, N.69, R.72, R.193, R.199, S.201 Ligands: MG.6, PIS.7, 61G.8 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.19, B:I.20, B:W.63, B:W.63, B:W.63, B:W.63 Hydrogen bonds: B:N.69, B:R.72, B:S.201, B:S.201, A:G.241, A:F.242, A:G.243, A:G.243 Water bridges: B:R.193, B:R.199, B:R.199 Salt bridges: B:R.193, B:R.199

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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