SMTL ID : 3q2q.1

Crystal structure of geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum complexed with calcium and isoprenyl diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.1: 8 residues within 4Å: Chain A: T.111, L.112, D.115, D.119, L.172, Q.176, K.199 Ligands: CA.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.112, A:D.115, A:L.172 Water bridges: A:E.179, A:K.199 Salt bridges: A:K.199 DMA.7: 8 residues within 4Å: Chain B: T.111, L.112, D.115, D.119, L.172, Q.176, K.199 Ligands: CA.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.112, B:D.115, B:L.172 Water bridges: B:E.179, B:K.199 Salt bridges: B:K.199

6 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 3 residues within 4Å: Chain A: D.115, D.119 Ligands: DMA.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.115, A:D.119, A:D.119, H2O.8, H2O.8 CA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: E.302, S.305 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.302, A:E.302, A:S.305, H2O.2, H2O.3 CA.8: 3 residues within 4Å: Chain B: D.115, D.119 Ligands: DMA.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.115, B:D.119, B:D.119, H2O.16, H2O.16 CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.12: 2 residues within 4Å: Chain B: E.302, S.305 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.302, B:E.302, B:S.305, H2O.10, H2O.11

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: K.75, R.76, F.77, R.78, H.108 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.75, A:R.76, A:F.77, A:R.78, A:R.78 Water bridges: A:R.78 GOL.5: 3 residues within 4Å: Chain A: D.223, K.226, N.227 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.226, A:K.226, A:N.227 Water bridges: A:N.227, A:E.327 GOL.10: 5 residues within 4Å: Chain B: K.75, R.76, F.77, R.78, H.108 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.75, B:R.76, B:F.77, B:R.78, B:R.78 Water bridges: B:R.78 GOL.11: 3 residues within 4Å: Chain B: D.223, K.226, N.227 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.226, B:K.226, B:N.227 Water bridges: B:E.327, B:R.330

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

2011-01-12

Peptides

Geranylgeranyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Geranylgeranyl pyrophosphate synthase

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