SMTL ID : 4lfg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

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

IPE.1: 17 residues within 4Å: Chain A: S.75, L.76, D.79, D.85, R.90, M.146, Q.150, K.173, T.174, Q.211, D.214, D.218, K.228 Ligands: IPE.2, MG.3, MG.4, MG.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.76, A:D.79, A:K.173 Hydrogen bonds: A:Q.211 Water bridges: A:R.90, A:Q.150, A:Q.150, A:D.153, A:K.173, A:K.173, A:K.173, A:K.173 Salt bridges: A:R.90, A:K.173, A:K.228 IPE.2: 11 residues within 4Å: Chain A: G.38, K.39, R.42, H.72, L.76, R.91, T.174, F.210, Q.211, D.214 Ligands: IPE.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.76, A:T.174, A:F.210, A:D.214 Hydrogen bonds: A:K.39 Water bridges: A:G.38, A:G.38, A:K.39, A:R.40, A:R.42, A:R.42 Salt bridges: A:K.39, A:K.39, A:R.42, A:H.72, A:H.72, A:R.91 IPE.6: 14 residues within 4Å: Chain B: S.75, D.79, D.85, R.90, Q.150, K.173, T.174, Q.211, D.214, K.228 Ligands: IPE.7, MG.8, MG.9, MG.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:D.79, B:K.173 Hydrogen bonds: B:Q.211 Water bridges: B:D.85, B:D.85, B:Q.150, B:K.173, B:K.173, B:K.173, B:K.173, B:D.218, B:K.232, B:K.232 Salt bridges: B:R.90, B:K.173, B:K.228 IPE.7: 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.6 18 PLIP interactions: 18 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:K.39, B:K.39, B:R.40, B:R.42, B:R.42, B:R.90, B:R.213 Salt bridges: B:K.39, B:K.39, B:R.42, B:H.72, B:H.72, B:R.91

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.79, D.85, D.153 Ligands: IPE.1, MG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.79, A:D.85, H2O.2, H2O.4, H2O.4 MG.4: 4 residues within 4Å: Chain A: D.79, D.85 Ligands: IPE.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, A:D.85, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain A: D.214, D.218, K.228 Ligands: IPE.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.214, A:D.218, H2O.5, H2O.7 MG.8: 3 residues within 4Å: Chain B: D.214, D.218 Ligands: IPE.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.214, H2O.11, H2O.18, H2O.18 MG.9: 5 residues within 4Å: Chain B: D.79, D.85, D.153 Ligands: IPE.6, MG.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.79, B:D.85, H2O.12, H2O.14, H2O.17 MG.10: 4 residues within 4Å: Chain B: D.79, D.85 Ligands: IPE.6, MG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.79, B:D.85, H2O.11, H2O.11

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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