SMTL ID : 1n23.1

(+)-Bornyl diphosphate synthase: Complex with Mg, pyrophosphate, and (1R,4S)-2-azabornane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.302, D.306, E.455 Ligands: MG.2, POP.5 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.302, A:D.306, H2O.3, H2O.3, POP.5 MG.2: 4 residues within 4Å: Chain A: D.302, D.306 Ligands: MG.1, POP.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.302, A:D.306, H2O.3, H2O.3, H2O.3 MG.3: 5 residues within 4Å: Chain A: R.444, D.447, T.451, E.455 Ligands: POP.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.447, A:T.451, A:E.455, H2O.3 MG.6: 5 residues within 4Å: Chain B: D.302, D.306, E.380 Ligands: MG.7, POP.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.302, B:D.306, H2O.7, H2O.7, H2O.7 MG.7: 4 residues within 4Å: Chain B: D.302, D.306 Ligands: MG.6, POP.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.302, B:D.306, H2O.7, H2O.7 MG.8: 4 residues within 4Å: Chain B: D.447, T.451, E.455 Ligands: POP.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:T.451, B:E.455, H2O.7

2 x 2BN: (1R,4S)-2-AZABORNANE(Non-covalent)

2BN.4: 6 residues within 4Å: Chain A: T.299, V.403, A.404, Y.523, F.529 Ligands: POP.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.403, A:A.404, A:F.529 2BN.9: 10 residues within 4Å: Chain B: R.265, W.274, I.295, T.299, V.403, A.404, D.447, Y.523, F.529 Ligands: POP.10 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.274, B:V.403, B:A.404, B:F.529

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 13 residues within 4Å: Chain A: R.265, D.302, D.306, R.444, D.447, T.451, E.455, D.460, K.463 Ligands: MG.1, MG.2, MG.3, 2BN.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.451 Water bridges: A:R.265, A:R.444, A:R.458, A:R.458, A:R.458, A:R.458, A:K.463, A:D.527 Salt bridges: A:R.265, A:R.444, A:K.463 POP.10: 12 residues within 4Å: Chain B: R.265, D.302, D.306, R.444, D.447, T.451, E.455, K.463 Ligands: MG.6, MG.7, MG.8, 2BN.9 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.455, B:E.455 Water bridges: B:R.265, B:R.265, B:S.402, B:R.444, B:D.447, B:T.451, B:R.458, B:R.458, B:R.458, B:K.463, B:K.463 Salt bridges: B:R.265, B:R.444, 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 cyclase. 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
B

(+)-bornyl diphosphate synthase

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