SMTL ID : 4lfe.1

Crystal structure of geranylgeranyl diphosphate synthase sub1274 (target efi-509455) from streptococcus uberis 0140j with bound magnesium and isopentyl diphosphate, partially liganded complex;

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

3 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.1: 10 residues within 4Å: Chain A: S.75, L.76, D.79, D.85, R.90, M.146, Q.150, K.173 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.76, A:D.79, A:K.173 Water bridges: A:D.87, A:D.87, A:Q.150, A:D.153, A:K.173, A:Q.211, A:D.218 Salt bridges: A:R.90, A:K.173 IPE.4: 14 residues within 4Å: Chain B: L.76, D.79, D.85, R.90, Q.150, K.173, T.174, Q.211, D.214, K.228 Ligands: IPE.5, MG.6, MG.7, MG.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.76, B:D.79, B:K.173 Hydrogen bonds: B:D.79, B:Q.211, B:D.214 Water bridges: B:Q.150, B:Q.150, B:K.173, B:K.173, B:K.173, B:D.218, B:K.228, B:K.232, B:K.232, B:K.232, B:K.232 Salt bridges: B:R.90, B:K.173, B:K.228 IPE.5: 11 residues within 4Å: Chain B: G.38, K.39, R.42, H.72, L.76, R.91, T.174, F.210, Q.211, D.214 Ligands: IPE.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.76, B:T.174, B:F.210, B:D.214 Hydrogen bonds: B:K.39 Water bridges: B:G.38, B:G.38, B:R.40, B:R.42, B:R.42 Salt bridges: B:K.39, B:K.39, B:R.42, B:H.72, B:H.72, B:R.91

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.79, D.85, D.153 Ligands: IPE.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.79, A:D.85, H2O.2, H2O.3, H2O.3 MG.3: 5 residues within 4Å: Chain A: D.79, D.85, R.90 Ligands: IPE.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, A:D.85, H2O.1, H2O.2 MG.6: 3 residues within 4Å: Chain B: D.214, D.218 Ligands: IPE.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.214, H2O.5, H2O.5, H2O.6 MG.7: 4 residues within 4Å: Chain B: D.79, D.85 Ligands: IPE.4, MG.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.79, B:D.85, H2O.5, H2O.7, H2O.8 MG.8: 4 residues within 4Å: Chain B: D.79, D.85 Ligands: IPE.4, MG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.79, B:D.85, H2O.6, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal Structure of Geranylgeranyl Diphosphate Synthase from Streptococcus Uberis 0140J. To be Published

Release Date

2013-07-10

Peptides

Geranylgeranyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranylgeranyl diphosphate synthase

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