SMTL ID : 3p41.1

Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5 complexed with magnesium and isoprenyl pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: Q.227, D.231 Ligands: POP.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.231, H2O.2, H2O.3, H2O.3, H2O.3 MG.2: 4 residues within 4Å: Chain A: D.91, D.97 Ligands: MG.3, DMA.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.91, A:D.97, H2O.1, H2O.4, H2O.4 MG.3: 5 residues within 4Å: Chain A: D.91, D.97, R.102 Ligands: MG.2, DMA.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.91, A:D.97, H2O.3, H2O.4 MG.9: 3 residues within 4Å: Chain B: Q.227, D.231 Ligands: POP.14 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.231, H2O.7, H2O.8, H2O.9, H2O.9 MG.10: 4 residues within 4Å: Chain B: D.91, D.97 Ligands: MG.11, DMA.13 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.91, B:D.97, H2O.6, H2O.9, H2O.9 MG.11: 5 residues within 4Å: Chain B: D.91, D.97, R.102 Ligands: MG.10, DMA.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.91, B:D.97, H2O.9, H2O.9

4 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.4: 10 residues within 4Å: Chain A: G.51, K.52, R.53, V.54, R.55, H.84, R.103, I.193, F.226, I.298 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.54, A:I.193, A:F.226, A:I.298 Hydrogen bonds: A:K.52, A:R.53, A:V.54 Water bridges: A:R.55, A:R.55, A:R.103, A:R.103, A:R.103 Salt bridges: A:R.55, A:R.55, A:H.84, A:H.84, A:R.103, A:R.103 DMA.5: 11 residues within 4Å: Chain A: S.87, L.88, D.91, D.97, R.102, M.161, Q.165, K.188 Ligands: MG.2, MG.3, POP.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.88, A:D.91 Water bridges: A:D.97, A:R.102, A:R.102, A:D.168, A:D.168, A:D.168, A:K.188, A:K.188 Salt bridges: A:R.102, A:K.188 DMA.12: 10 residues within 4Å: Chain B: G.51, K.52, R.53, V.54, R.55, H.84, R.103, I.193, F.226, I.298 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.54, B:I.193, B:F.226, B:I.298 Hydrogen bonds: B:K.52, B:R.53, B:V.54 Water bridges: B:R.55, B:R.55, B:R.103, B:R.103, B:R.103 Salt bridges: B:R.55, B:R.55, B:H.84, B:H.84, B:R.103, B:R.103 DMA.13: 11 residues within 4Å: Chain B: S.87, L.88, D.91, D.97, R.102, M.161, Q.165, K.188 Ligands: MG.10, MG.11, POP.14 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.88, B:D.91 Hydrogen bonds: B:D.97 Water bridges: B:D.97, B:R.102, B:R.102, B:Q.165, B:D.168, B:K.188, B:K.188, B:K.188 Salt bridges: B:R.102, B:K.188

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

POP.6: 6 residues within 4Å: Chain A: D.168, H.185, K.188, Q.227 Ligands: MG.1, DMA.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.227 Water bridges: A:D.97, A:D.168, A:D.168, A:K.188 Salt bridges: A:H.185, A:K.188, A:K.188 POP.14: 6 residues within 4Å: Chain B: D.168, H.185, K.188, Q.227 Ligands: MG.9, DMA.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.227 Water bridges: B:D.97, B:D.168, B:D.168, B:K.188 Salt bridges: B:H.185, B:K.188, B:K.188

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: D.98, D.99, D.100, L.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.99, A:D.100, A:L.101, A:L.101 GOL.15: 4 residues within 4Å: Chain B: D.98, D.99, D.100, L.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.100, B:L.101, B:L.101

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 3 residues within 4Å: Chain A: T.30, A.31, R.44 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: T.30, A.31, R.44 Ligand excluded by PLIP

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

2010-10-20

Peptides

Geranyltranstransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Geranyltranstransferase