SMTL ID : 2ong.1

Crystal Structure of of limonene synthase with 2-fluorogeranyl diphosphate (FGPP).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.296, D.300, E.374, D.453 Ligands: MN.2, FPG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.296, A:D.300 MN.2: 6 residues within 4Å: Chain A: D.296, D.300, R.451, D.453 Ligands: MN.1, FPG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.296, A:D.300 MN.3: 3 residues within 4Å: Chain A: D.440, T.444 Ligands: FPG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.440, A:T.444 MN.7: 5 residues within 4Å: Chain B: D.296, D.300, E.374 Ligands: MN.8, FPG.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.296, B:D.300 MN.8: 5 residues within 4Å: Chain B: R.259, D.296, D.300 Ligands: MN.7, FPG.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.296, B:D.300 MN.9: 3 residues within 4Å: Chain B: D.440, T.444 Ligands: FPG.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.440

2 x FPG: (1S)-1-[(1R)-1-FLUOROETHYL]-1,5-DIMETHYLHEXYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

FPG.4: 21 residues within 4Å: Chain A: R.259, C.265, W.268, N.289, I.292, T.293, D.296, D.300, Y.371, I.397, M.402, R.437, D.440, T.444, D.453, K.456, Y.517, H.523 Ligands: MN.1, MN.2, MN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.268, A:N.289, A:I.292, A:D.296 Salt bridges: A:R.259, A:R.437, A:K.456 Halogen bonds: A:I.397 FPG.10: 17 residues within 4Å: Chain B: R.259, W.268, I.292, T.293, D.296, D.300, S.396, I.397, R.437, D.440, T.444, K.456, Y.517, H.523 Ligands: MN.7, MN.8, MN.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.268, B:I.292, B:I.397, B:H.523 Hydrogen bonds: B:T.444 Salt bridges: B:R.259, B:R.437, B:K.456

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.5: 7 residues within 4Å: Chain A: E.387, L.390, R.430, F.434, L.479, E.482, K.486 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.387, A:R.430, A:K.486 Salt bridges: A:E.387 BTB.6: 1 residues within 4Å: Chain A: E.170 No protein-ligand interaction detected (PLIP) BTB.11: 5 residues within 4Å: Chain B: E.387, R.430, L.479, E.482, K.486 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.387, B:R.430, B:R.430, B:H.475, B:K.486 Water bridges: B:K.486 BTB.12: 2 residues within 4Å: Chain B: R.162, K.474 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.166, B:T.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hyatt, D.C. et al., Structure of limonene synthase, a simple model for terpenoid cyclase catalysis. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-03-06

Peptides

4S-limonene synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4S-limonene synthase

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