SMTL ID : 1n22.1

(+)-Bornyl Diphosphate Synthase: Complex with Mg, pyrophosphate, and (4R)-7-aza-7,8-dihydrolimonene

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.302, D.306, E.380 Ligands: MG.2, 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.2: 6 residues within 4Å: Chain A: D.302, D.306, E.455, R.458 Ligands: MG.1, POP.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.302, A:D.306, 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: 4 residues within 4Å: Chain B: D.302, D.306 Ligands: MG.7, POP.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.302, B:D.306, H2O.6 MG.7: 5 residues within 4Å: Chain B: D.302, D.306, E.380 Ligands: MG.6, POP.11 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.302, B:D.306, H2O.6, H2O.6, H2O.6 MG.8: 4 residues within 4Å: Chain B: D.447, E.455 Ligands: MG.9, POP.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.447, B:E.455, H2O.6 MG.9: 4 residues within 4Å: Chain B: D.447, S.452 Ligands: MG.8, POP.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.447, B:S.452

2 x 7A8: (1R)-DIMETHYL-(4-METHYL-CYCLOHEX-3-ENYL)-AMINE(Non-covalent)

7A8.4: 10 residues within 4Å: Chain A: W.274, I.295, T.299, D.302, Y.377, S.402, V.403, A.404, F.529 Ligands: POP.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.274, A:I.295, A:A.404, A:F.529 Salt bridges: A:D.302, A:D.447 7A8.10: 10 residues within 4Å: Chain B: W.274, I.295, T.299, D.302, Y.377, V.403, A.404, I.408, L.443 Ligands: POP.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.274, B:W.274, B:I.295, B:A.404, B:I.408, B:L.443 Salt bridges: B:D.302

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, 7A8.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.451 Water bridges: A:Y.11, A:R.265, A:R.265, A:D.306, A:R.444, A:R.444, A:D.447, A:E.455, 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.11: 14 residues within 4Å: Chain B: R.265, D.302, D.306, R.444, D.447, S.452, E.455, D.460, K.463 Ligands: MG.6, MG.7, MG.8, MG.9, 7A8.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.452, B:S.452 Water bridges: B:D.448, B:K.463, B:K.463, 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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