SMTL ID : 2j1p.1

GERANYLGERANYL DIPHOSPHATE SYNTHASE FROM SINAPIS ALBA IN COMPLEX WITH GGPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x GRG: GERANYLGERANYL DIPHOSPHATE(Non-covalent)

GRG.1: 18 residues within 4Å: Chain A: G.52, K.53, R.56, H.85, M.87, S.88, H.91, D.92, R.104, I.157, L.162, V.163, Q.166, K.192, T.193 Chain B: L.120, D.123, S.127 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.91, A:D.92, A:I.157, A:L.162, A:L.162, A:V.163, A:Q.166, A:Q.166, B:L.120 Hydrogen bonds: A:K.53 Water bridges: A:G.51, A:R.54, A:R.54, A:R.56, A:R.104 Salt bridges: A:K.53, A:K.53, A:R.56, A:H.85, A:H.85, A:R.104

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.2: 9 residues within 4Å: Chain A: L.120, D.123 Chain B: S.88, H.91, D.92, M.97, L.162, V.163, Q.166 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.162, B:V.163 Hydrogen bonds: B:H.91, B:D.92 Water bridges: B:Q.166 PGO.3: 3 residues within 4Å: Chain B: F.128, E.131, H.132 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.128 Hydrogen bonds: B:E.131, B:H.132 Water bridges: B:E.131, B:S.135

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 7 residues within 4Å: Chain B: R.56, H.85, S.88, L.162, K.192, T.193, L.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.85, B:S.88 BME.5: 8 residues within 4Å: Chain B: Y.46, S.47, L.89, I.90, D.93, R.103, T.108, N.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.109 Water bridges: B:Y.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kloer, D.P. et al., Structure and Reaction Geometry of Geranylgeranyl Diphosphate Synthase from Sinapis Alba. Biochemistry (2006)

Release Date

2007-01-02

Peptides

GERANYLGERANYL PYROPHOSPHATE SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GERANYLGERANYL PYROPHOSPHATE SYNTHETASE