SMTL ID : 3rbm.2 (1 other biounit)

Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH -703

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.287, D.291, D.305 Ligands: B73.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.287 MG.2: 5 residues within 4Å: Chain A: D.126, D.130, Q.195, D.198 Ligands: B73.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, A:D.130, H2O.2, H2O.3 MG.3: 3 residues within 4Å: Chain A: D.126, D.130 Ligands: B73.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.3 MG.6: 4 residues within 4Å: Chain B: D.287, D.291, D.305 Ligands: B73.9 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.287, H2O.5, H2O.5 MG.7: 6 residues within 4Å: Chain B: D.126, D.130, Q.195, D.198 Ligands: MG.8, B73.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.5, H2O.5, H2O.5 MG.8: 4 residues within 4Å: Chain B: D.126, D.130 Ligands: MG.7, B73.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.5, H2O.5

2 x B73: 3-(2,2-diphosphonoethyl)-1-dodecyl-1H-imidazol-3-ium(Non-covalent)

B73.4: 20 residues within 4Å: Chain A: F.122, A.125, D.126, D.130, R.135, V.156, T.191, Q.195, K.243, T.244, Q.284, D.287, K.301 Chain B: V.153, N.154, L.157 Ligands: MG.1, MG.2, MG.3, B73.9 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.125, A:V.156, A:T.191, A:Q.195, B:L.157, B:L.157 Hydrogen bonds: A:R.135, A:R.135, A:K.243, A:Q.284, A:K.301, A:K.301 Water bridges: A:K.243, A:K.243 B73.9: 22 residues within 4Å: Chain A: V.153, N.154, L.157 Chain B: F.122, A.125, D.126, D.130, R.135, V.156, L.157, T.191, I.192, Q.195, K.243, T.244, Q.284, D.287, K.301 Ligands: B73.4, MG.6, MG.7, MG.8 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.122, B:F.122, B:A.125, B:V.156, B:T.191, B:I.192, B:Q.195, A:V.153, A:L.157, A:L.157 Hydrogen bonds: B:R.135, B:R.135, B:K.243, B:Q.284, B:K.301, B:K.301 Water bridges: B:D.130, B:D.130, B:D.130, B:Q.195, B:Q.195, B:K.243, B:K.243

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: G.80, K.81, Q.119, R.136 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.81, A:Q.119 Water bridges: A:G.80, A:K.81, A:N.82, A:R.84 Salt bridges: A:K.81, A:R.136 SO4.10: 4 residues within 4Å: Chain B: G.80, K.81, Q.119, R.136 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.81, B:Q.119 Water bridges: B:N.82 Salt bridges: B:K.81, B:R.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

No, J.H. et al., Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-02-29

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Farnesyl pyrophosphate synthase

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