SMTL ID : 4gp2.1

Crystal structure of ISOPRENOID SYNTHASE A3MSH1 (TARGET EFI-501992) from pyrobaculum calidifontis complexed with DMAPP and Magnesium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.85, D.89 Ligands: MG.2, DMA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.85, A:D.89, H2O.3, H2O.4 MG.2: 5 residues within 4Å: Chain A: D.85, D.89, E.148 Ligands: MG.1, DMA.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.85, A:D.89, H2O.3, H2O.4, H2O.4 MG.5: 2 residues within 4Å: Chain A: D.225, D.229 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.225, A:D.229, H2O.2, H2O.3, H2O.4, H2O.4 MG.6: 5 residues within 4Å: Chain B: D.85, D.89, E.148 Ligands: MG.7, DMA.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.85, B:D.89, H2O.8, H2O.8, H2O.8 MG.7: 5 residues within 4Å: Chain B: D.85, D.89, R.94 Ligands: MG.6, DMA.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.85, B:D.89, H2O.8, H2O.9 MG.8: 3 residues within 4Å: Chain B: D.225, D.229, K.243 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.225, B:D.229, H2O.7, H2O.9, H2O.9, H2O.9

4 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.3: 12 residues within 4Å: Chain A: S.81, L.82, D.85, D.89, R.94, E.148, D.151, K.184, K.249 Ligands: MG.1, MG.2, DMA.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.82, A:D.85, A:K.184 Hydrogen bonds: A:D.151 Water bridges: A:R.94, A:K.184, A:K.184, A:K.243, A:K.249 Salt bridges: A:R.94, A:K.184, A:K.249 DMA.4: 8 residues within 4Å: Chain A: G.45, K.46, R.49, H.78, R.95, T.185, Q.222 Ligands: DMA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.185 Hydrogen bonds: A:K.46 Water bridges: A:K.46, A:R.49, A:R.49, A:R.95 Salt bridges: A:K.46, A:K.46, A:R.49, A:H.78, A:H.78, A:R.95 DMA.9: 13 residues within 4Å: Chain B: S.81, L.82, D.85, D.89, R.94, I.144, D.151, K.184, K.243, K.249 Ligands: MG.6, MG.7, DMA.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.82, B:D.85, B:I.144, B:K.184 Water bridges: B:R.94, B:R.94, B:D.151, B:K.184, B:K.184, B:K.184, B:Q.222, B:K.243, B:K.243, B:K.249, B:K.249, B:K.249 Salt bridges: B:R.94, B:K.184, B:K.243, B:K.249 DMA.10: 9 residues within 4Å: Chain B: G.45, K.46, R.49, H.78, R.95, T.185, F.221, Q.222 Ligands: DMA.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.221 Hydrogen bonds: B:K.46 Water bridges: B:K.46, B:R.47, B:R.49 Salt bridges: B:K.46, B:K.46, B:R.49, B:H.78, B:H.78, B:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Isoprenoid Synthase from Pyrobaculum Calidifontis. To be Published

Release Date

2012-10-10

Peptides

Polyprenyl synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Polyprenyl synthetase

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