SMTL ID : 3oyr.1

Crystal structure of polyprenyl synthase from Caulobacter crescentus CB15 complexed with calcium and isoprenyl diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

POP.1: 6 residues within 4Å: Chain A: G.64, K.66, R.67, L.68, R.69, H.98 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.67, A:L.68 Water bridges: A:R.69 Salt bridges: A:R.69, A:R.69, A:H.98, A:H.98

2 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.2: 12 residues within 4Å: Chain B: G.65, K.66, R.69, H.98, L.102, R.114, R.115, T.192, F.228, Q.229, D.232 Ligands: DMA.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.102, B:T.192, B:F.228 Hydrogen bonds: B:K.66 Water bridges: B:G.65, B:G.65, B:R.67, B:R.67, B:R.69, B:R.69, B:K.246, B:K.246, B:R.343 Salt bridges: B:K.66, B:K.66, B:R.69, B:H.98, B:H.98, B:R.115 DMA.5: 12 residues within 4Å: Chain B: T.101, L.102, D.105, D.109, R.114, K.191, Q.229, D.232, K.246 Ligands: DMA.2, CA.3, CA.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.102, B:D.105 Hydrogen bonds: B:Q.229 Water bridges: B:D.106, B:S.111, B:S.111, B:K.191, B:K.191, B:D.233, B:K.246, B:D.251, B:D.251 Salt bridges: B:R.114, B:K.191, B:K.246, B:K.256

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain B: D.105, D.109 Ligands: DMA.5 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.105, B:D.109, H2O.3, H2O.4 CA.4: 3 residues within 4Å: Chain B: D.232, D.236 Ligands: DMA.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.232, H2O.3, H2O.4, H2O.5

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

2010-10-13

Peptides

Trans-isoprenyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trans-isoprenyl diphosphate synthase