SMTL ID : 1n21.1

(+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3-aza-2,3-dihydrogeranyl diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.302, D.306, Y.377, E.380 Ligands: MG.3, 3AG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.302, A:D.306, H2O.1, H2O.1 MG.2: 4 residues within 4Å: Chain A: D.447, T.451, E.455 Ligands: 3AG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:T.451, A:E.455, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.302, D.306, E.455 Ligands: MG.1, 3AG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.302, A:D.306, H2O.1, H2O.1, H2O.1 MG.5: 6 residues within 4Å: Chain B: D.302, D.306, Y.377, E.380 Ligands: MG.7, 3AG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.302, B:D.306, H2O.2, H2O.2 MG.6: 4 residues within 4Å: Chain B: D.447, T.451, E.455 Ligands: 3AG.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:T.451, B:E.455, H2O.2 MG.7: 5 residues within 4Å: Chain B: D.302, D.306, E.455 Ligands: MG.5, 3AG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.302, B:D.306, H2O.2, H2O.2, H2O.2

2 x 3AG: 2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE(Non-covalent)

3AG.4: 19 residues within 4Å: Chain A: R.265, W.274, I.295, T.299, D.302, D.306, V.403, I.408, L.443, R.444, D.447, T.451, E.455, K.463, Y.523, F.529 Ligands: MG.1, MG.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.274, A:I.295, A:I.408, A:L.443, A:F.529 Hydrogen bonds: A:T.451 Water bridges: A:D.302, A:S.402, A:R.444, A:R.444, A:R.444, A:R.458, A:R.458, A:K.463 Salt bridges: A:R.265, A:R.444, A:D.447, A:K.463 3AG.8: 19 residues within 4Å: Chain B: R.265, W.274, I.295, T.299, D.302, D.306, V.403, I.408, L.443, R.444, D.447, T.451, E.455, K.463, Y.523, F.529 Ligands: MG.5, MG.6, MG.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:W.274, B:I.295, B:I.408, B:L.443, B:F.529 Hydrogen bonds: B:E.455 Water bridges: B:D.302, B:S.402, B:R.444, B:R.444, B:R.444, B:R.458, B:R.458, B:K.463 Salt bridges: B:R.265, B:R.444, B:D.447, B:K.463

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whittington, D.A. et al., Bornyl diphosphate synthase: Structure and strategy for carbocation manipulation by a terpenoid synthase. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-11-27

Peptides

(+)-bornyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

(+)-bornyl diphosphate synthase

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