SMTL ID : 3ez3.2 (1 other biounit)

Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.1: 13 residues within 4Å: Chain A: D.126, D.130, R.135, Q.195, K.243, T.244, Q.284, D.287, K.301 Ligands: IPE.2, MG.3, MG.4, MG.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.135, A:R.135, A:Q.284, A:D.287, A:D.287 Water bridges: A:Q.195 ZOL.6: 14 residues within 4Å: Chain B: L.123, D.126, D.130, R.135, Q.195, K.243, T.244, Q.284, D.287, K.301 Ligands: IPE.7, MG.8, MG.9, MG.10 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.135, B:R.135, B:Q.284, B:D.287 Water bridges: B:D.127, B:D.130, B:Q.195, B:K.243, B:K.243, B:K.243, B:K.243, B:D.287, B:D.291 pi-Cation interactions: B:K.243

2 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.2: 12 residues within 4Å: Chain A: G.80, K.81, R.84, Q.119, R.136, T.244, Y.247, S.248, F.283, Q.284, D.287 Ligands: ZOL.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.244, A:F.283, A:D.287 Hydrogen bonds: A:K.81, A:R.84, A:Q.119 Water bridges: A:K.81, A:N.82, A:N.82, A:N.82, A:R.135, A:R.135, A:K.301 Salt bridges: A:K.81, A:K.81, A:R.84, A:R.136 IPE.7: 12 residues within 4Å: Chain B: G.80, K.81, R.84, Q.119, R.136, T.244, Y.247, S.248, F.283, Q.284, D.287 Ligands: ZOL.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.244, B:F.283 Hydrogen bonds: B:K.81, B:R.84, B:Q.119 Water bridges: B:K.81, B:K.81, B:N.82, B:K.301 Salt bridges: B:K.81, B:K.81, B:R.84, B:R.136

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: ZOL.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.4 MG.4: 5 residues within 4Å: Chain A: D.126, D.130, D.198 Ligands: ZOL.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.1, H2O.3 MG.5: 2 residues within 4Å: Chain A: D.287 Ligands: ZOL.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.287, H2O.1, H2O.3, H2O.4 MG.8: 5 residues within 4Å: Chain B: D.126, D.130, D.198 Ligands: ZOL.6, MG.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.6, H2O.6, H2O.8 MG.9: 5 residues within 4Å: Chain B: D.126, D.130, R.135 Ligands: ZOL.6, MG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.6, H2O.6 MG.10: 2 residues within 4Å: Chain B: D.287 Ligands: ZOL.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.287, H2O.7, H2O.7, H2O.10

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 7 residues within 4Å: Chain B: D.291, I.292, G.303, S.304, D.305, I.306, D.346 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.305, B:I.306, B:D.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wernimont, A.K. et al., Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound. TO BE PUBLISHED

Release Date

2008-12-02

Peptides

Farnesyl pyrophosphate synthase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Farnesyl pyrophosphate synthase, putative

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