SMTL ID : 3qqv.1

Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium glutamicum complexed with isoprenyl diphosphate and magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.108, D.112, D.194 Ligands: MG.2, DMA.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.108, A:D.112, H2O.1, H2O.1 MG.2: 6 residues within 4Å: Chain A: D.108, D.112, R.117, K.271 Ligands: MG.1, DMA.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.108, A:D.112, H2O.2, H2O.3 MG.7: 5 residues within 4Å: Chain B: D.108, D.112, D.194 Ligands: MG.8, DMA.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.108, B:D.112, H2O.7, H2O.7 MG.8: 6 residues within 4Å: Chain B: D.108, D.112, R.117, K.271 Ligands: MG.7, DMA.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.108, B:D.112, H2O.8, H2O.8

4 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.3: 8 residues within 4Å: Chain A: G.62, K.63, I.65, R.66, Q.101, R.118, Q.254 Ligands: DMA.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.63, A:Q.101 Water bridges: A:G.62, A:R.64, A:R.64, A:R.66 Salt bridges: A:K.63, A:K.63, A:R.66, A:R.118 DMA.4: 12 residues within 4Å: Chain A: A.104, D.108, D.112, R.117, V.187, Q.191, K.215, K.271, K.281 Ligands: MG.1, MG.2, DMA.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.104, A:D.108, A:V.187, A:Q.191, A:K.215 Water bridges: A:D.112, A:R.117, A:K.281 Salt bridges: A:R.117, A:K.215, A:K.271, A:K.271, A:K.281, A:K.281 DMA.9: 8 residues within 4Å: Chain B: G.62, K.63, I.65, R.66, Q.101, R.118, Q.254 Ligands: DMA.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.63, B:Q.101 Water bridges: B:G.62, B:R.64, B:R.64, B:R.66 Salt bridges: B:K.63, B:K.63, B:R.66, B:R.118 DMA.10: 12 residues within 4Å: Chain B: A.104, D.108, D.112, R.117, V.187, Q.191, K.215, K.271, K.281 Ligands: MG.7, MG.8, DMA.9 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.104, B:D.108, B:V.187, B:Q.191, B:K.215 Water bridges: B:R.117, B:R.117, B:K.281 Salt bridges: B:R.117, B:K.215, B:K.271, B:K.271, B:K.281, B:K.281

2 x UNL: UNKNOWN LIGAND

UNL.5: 4 residues within 4Å: Chain A: R.256, E.334, E.370, R.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.370 Water bridges: A:R.256, A:R.256 UNL.11: 4 residues within 4Å: Chain B: R.256, E.334, E.370, R.372 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.370 Water bridges: B:R.256, B:R.256

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: S.83, S.84, E.85, E.171, R.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.84, A:S.84, A:R.175, A:R.175 GOL.12: 5 residues within 4Å: Chain B: S.83, S.84, E.85, E.171, R.175 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.84, B:S.84, B:E.85, B:R.175, B:R.175

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

2011-03-02

Peptides

Geranylgeranyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Geranylgeranyl pyrophosphate synthase

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