SMTL ID : 3pde.1 (1 other biounit)

Crystal structure of geranylgeranyl pyrophosphate synthase from Lactobacillus brevis atcc 367 complexed with isoprenyl diphosphate and magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.1: 10 residues within 4Å: Chain A: G.48, K.49, R.52, H.83, L.87, R.102, T.185, F.221, D.225 Ligands: DMA.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.49 Water bridges: A:K.49, A:K.49, A:R.50, A:R.50, A:R.52 Salt bridges: A:K.49, A:K.49, A:R.52, A:H.83, A:H.83, A:R.102 DMA.2: 11 residues within 4Å: Chain A: S.86, L.87, D.90, D.96, R.101, M.157, Q.161, K.184 Ligands: DMA.1, MG.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.87, A:D.90, A:K.184 Water bridges: A:D.96, A:R.101, A:Q.161, A:D.164, A:D.164, A:K.184, A:D.225, A:D.225, A:D.229, A:D.229 Salt bridges: A:R.101, A:K.184 DMA.6: 9 residues within 4Å: Chain B: G.48, K.49, R.52, H.83, L.87, R.102, T.185, F.221 Ligands: DMA.9 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.49 Water bridges: B:K.49, B:K.49, B:R.50, B:R.52, B:R.52, B:Y.294, B:Y.294, B:R.299 Salt bridges: B:K.49, B:K.49, B:R.52, B:H.83, B:H.83, B:R.102 DMA.9: 11 residues within 4Å: Chain B: S.86, L.87, D.90, D.96, R.101, M.157, Q.161, K.184 Ligands: DMA.6, MG.7, MG.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.87, B:D.90, B:K.184 Water bridges: B:D.96, B:D.96, B:D.96, B:D.98, B:Q.161, B:Q.161, B:D.164, B:D.164, B:K.184, B:K.184 Salt bridges: B:R.101, B:K.184

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.90, D.96 Ligands: DMA.2, MG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.90, A:D.96, H2O.6, H2O.9, H2O.9 MG.4: 5 residues within 4Å: Chain A: D.90, D.96, R.101 Ligands: DMA.2, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.90, A:D.96, H2O.8, H2O.9 MG.7: 5 residues within 4Å: Chain B: D.90, D.96, D.164 Ligands: MG.8, DMA.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.90, B:D.96, H2O.15, H2O.17 MG.8: 5 residues within 4Å: Chain B: D.90, D.96, R.101 Ligands: MG.7, DMA.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.90, B:D.96, H2O.15, H2O.17

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: L.276, Q.277, L.279, P.280, T.281, S.282, R.285, D.286, A.289 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.279, A:S.282, A:D.286, A:D.286 Water bridges: A:Q.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallrapp, F.H. et al., Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2010-11-17

Peptides

Farnesyl-diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl-diphosphate synthase

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