SMTL ID : 3ldw.1 (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 2.47 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 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.135, A:R.135, A:Y.247, A:Q.284, A:Q.284, A:D.287 Water bridges: A:Q.195, A:K.243, A:K.243, A:K.243, A:K.243, A:K.243, A:D.291, A:D.291, A:D.291 pi-Cation interactions: A:K.243 ZOL.8: 14 residues within 4Å: Chain B: D.126, D.130, R.135, Q.195, K.243, T.244, Q.284, D.287, K.301 Ligands: IPE.9, MG.10, MG.11, MG.12, EDO.14 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.135, B:R.135, B:Q.284, B:Q.284, B:D.287, B:D.287 Water bridges: B:Q.195, B:K.243, B:K.243, B:K.301

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, F.283, Q.284, D.287, K.301 Ligands: ZOL.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.283, A:D.287 Hydrogen bonds: A:K.81, A:R.84, A:Q.119 Water bridges: A:K.81, A:K.81, A:K.81, A:N.82, A:N.83, A:N.83, A:R.135 Salt bridges: A:K.81, A:K.81, A:R.84, A:R.136 IPE.9: 11 residues within 4Å: Chain B: G.80, K.81, R.84, Q.119, R.136, Y.247, F.283, Q.284, D.287, K.301 Ligands: ZOL.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.283, B:D.287 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 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.126, A:D.130, H2O.2, H2O.3 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.2, H2O.3 MG.5: 3 residues within 4Å: Chain A: D.287, D.305 Ligands: ZOL.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.287, H2O.1, H2O.2, H2O.6 MG.10: 5 residues within 4Å: Chain B: D.126, D.130, D.198 Ligands: ZOL.8, MG.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.6, H2O.7, H2O.8 MG.11: 3 residues within 4Å: Chain B: D.287 Ligands: ZOL.8, EDO.14 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.287, H2O.6, H2O.7, H2O.7 MG.12: 5 residues within 4Å: Chain B: D.126, D.130 Ligands: ZOL.8, MG.10, EDO.14 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.7, H2O.8

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: E.58, E.60 Chain B: N.229, N.232, V.235 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.232, A:E.58 Water bridges: A:E.60 EDO.14: 8 residues within 4Å: Chain B: D.291, K.301, V.302, G.303 Ligands: ZOL.8, MG.11, MG.12, GOL.13 7 PLIP interactions: 7 interactions with chain B Water bridges: B:D.127, B:R.135, B:R.135, B:K.301, B:S.304, B:S.304, B:S.304

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: K.131, G.132, E.133, Y.139, Y.142, L.143 Chain B: I.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.142 GOL.13: 9 residues within 4Å: Chain B: L.290, D.291, G.294, S.296, T.299, K.301, V.302, G.303 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.290, B:G.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Artz, J.D. et al., Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites. J.Biol.Chem. (2011)

Release Date

2010-11-17

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase

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