SMTL ID : 3aq0.2 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.107, D.111, E.169, E.172 Ligands: FPP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.107, A:D.111 MG.2: 5 residues within 4Å: Chain A: D.107, D.108, D.111, R.116 Ligands: FPP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.107

1 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.3: 14 residues within 4Å: Chain A: I.99, S.103, H.106, D.107, L.110, D.111, R.116, L.165, V.166, E.169, K.193 Chain B: D.136 Ligands: MG.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.106, A:L.110, A:L.165, A:V.166, A:E.169, A:E.169 Salt bridges: A:R.116, A:K.193

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.4: 5 residues within 4Å: Chain A: G.50, K.51, R.54, H.100, R.117 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.51, A:R.54 Water bridges: A:R.116, A:R.116 Salt bridges: A:K.51, A:K.51, A:R.54, A:H.100, A:H.100, A:R.117 PPV.5: 5 residues within 4Å: Chain B: R.54, E.97, H.100, V.101, L.104 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.97, B:E.97 Water bridges: B:R.54 Salt bridges: B:R.54, B:H.100, B:H.100

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain A: T.167, T.170 Chain B: F.137, R.141 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.170, A:T.170, B:R.141

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
C

B
D

Geranyl diphosphate synthase

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