SMTL ID : 3aq0.4 (3 other biounits)

Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.1: 4 residues within 4Å: Chain A: Q.49, K.51, R.54, H.100 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.51, A:R.54 Salt bridges: A:K.51, A:R.54, A:H.100, A:H.100

2 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.2: 10 residues within 4Å: Chain A: F.53, I.57, I.198, F.230, L.339, R.342, V.343, R.346, N.347, K.348 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.53, A:F.53, A:F.53, A:I.198, A:F.230, A:F.230, A:V.343, A:R.346 Hydrogen bonds: A:N.347, A:K.348 Water bridges: A:R.342 Salt bridges: A:K.348 FPP.5: 15 residues within 4Å: Chain A: D.136 Chain B: A.102, S.103, H.106, D.107, L.110, D.111, R.116, V.162, L.165, V.166, E.169, K.193 Ligands: MG.3, MG.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.110, B:V.162, B:V.166, B:E.169, B:E.169, B:K.193 Salt bridges: B:R.116, B:K.193

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain B: D.107, D.111, E.169, E.172 Ligands: FPP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.107, B:D.111 MG.4: 4 residues within 4Å: Chain B: D.107, D.111, R.116 Ligands: FPP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.107

1 x ISY: 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid(Non-covalent)

ISY.6: 9 residues within 4Å: Chain B: G.50, K.51, F.53, R.54, H.100, R.117, T.194, I.198, F.230 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.53, B:T.194, B:I.198, B:F.230, B:F.230 Hydrogen bonds: B:K.51, B:K.51, B:K.51, B:K.51, B:R.54 Water bridges: B:R.54 Salt bridges: B:K.51, B:H.100, B:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, F.-L. et al., Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl pyrophosphate synthase. Plant Physiol. (2011)

Release Date

2011-01-19

Peptides

Geranyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Geranyl diphosphate synthase

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