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

Crystal structure of P. vivax geranylgeranyl diphosphate synthase complexed with BPH-811

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x K9H: {2-[5-(decyloxy)pyridin-3-yl]ethane-1,1-diyl}bis(phosphonic acid)(Non-covalent)

K9H.1: 21 residues within 4Å: Chain A: F.122, A.125, D.126, D.130, R.135, V.156, L.157, T.191, Q.195, K.243, T.244, Q.284, D.287, K.301 Chain B: V.153, N.154, L.157 Ligands: MG.2, MG.3, MG.4, K9H.6 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.122, A:A.125, A:D.126, A:V.156, A:L.157, A:T.191, A:Q.195, B:V.153, B:L.157, B:L.157 Hydrogen bonds: A:R.135, A:R.135, A:K.243, A:Q.284, A:K.301 K9H.6: 21 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, T.191, Q.195, K.243, T.244, Y.247, Q.284, D.287, K.301 Ligands: K9H.1, MG.7, MG.8, MG.9 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.122, B:A.125, B:V.156, B:T.191, B:Q.195, A:V.153, A:L.157, A:L.157, A:L.157 Hydrogen bonds: B:R.135, B:R.135, B:K.243, B:Q.284, B:K.301 pi-Cation interactions: B:K.243 K9H.11: 22 residues within 4Å: Chain C: F.122, A.125, D.126, D.130, R.135, V.156, L.157, T.191, Q.195, K.243, T.244, Y.247, Q.284, D.287, K.301 Chain D: V.153, N.154, L.157 Ligands: MG.12, MG.13, MG.14, K9H.16 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.122, C:D.126, C:V.156, C:Q.195, D:V.153, D:L.157, D:L.157, D:L.157 Hydrogen bonds: C:R.135, C:R.135, C:K.243, C:Q.284, C:K.301 pi-Cation interactions: C:K.243 K9H.16: 21 residues within 4Å: Chain C: V.153, N.154, L.157 Chain D: F.122, L.123, A.125, D.126, D.130, R.135, V.156, T.191, Q.195, K.243, T.244, Q.284, D.287, K.301 Ligands: K9H.11, MG.17, MG.18, MG.19 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.122, D:L.123, D:A.125, D:V.156, D:T.191, D:Q.195, C:V.153, C:L.157, C:L.157, C:L.157 Hydrogen bonds: D:R.135, D:R.135, D:K.243, D:Q.284, D:K.301

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.287, D.291, D.305 Ligands: K9H.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.287 MG.3: 4 residues within 4Å: Chain A: D.126, D.130 Ligands: K9H.1, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1 MG.4: 6 residues within 4Å: Chain A: D.126, D.130, Q.195, D.198 Ligands: K9H.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.126, A:D.130, A:D.130 MG.7: 4 residues within 4Å: Chain B: D.287, D.291, D.305 Ligands: K9H.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.287 MG.8: 3 residues within 4Å: Chain B: D.126, D.130 Ligands: K9H.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.126, B:D.130 MG.9: 5 residues within 4Å: Chain B: D.126, D.130, Q.195, D.198 Ligands: K9H.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.126, B:D.130, B:D.130, B:D.198 MG.12: 4 residues within 4Å: Chain C: D.287, D.291, D.305 Ligands: K9H.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.287 MG.13: 4 residues within 4Å: Chain C: D.126, D.130 Ligands: K9H.11, MG.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.126, C:D.130 MG.14: 6 residues within 4Å: Chain C: D.126, D.130, Q.195, D.198 Ligands: K9H.11, MG.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.126, C:D.130 MG.17: 4 residues within 4Å: Chain D: D.287, D.291, D.305 Ligands: K9H.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.287 MG.18: 4 residues within 4Å: Chain D: D.126, D.130 Ligands: K9H.16, MG.19 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.126, D:D.130 MG.19: 6 residues within 4Å: Chain D: D.126, D.130, Q.195, D.198 Ligands: K9H.16, MG.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.126, D:D.130

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

SO4.5: 5 residues within 4Å: Chain A: G.80, K.81, R.84, Q.119, R.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.81, A:R.84, A:Q.119 Salt bridges: A:K.81, A:R.136 SO4.10: 5 residues within 4Å: Chain B: G.80, K.81, R.84, Q.119, R.136 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.81, B:R.84, B:Q.119 Salt bridges: B:K.81, B:R.136 SO4.15: 6 residues within 4Å: Chain C: G.80, K.81, R.84, Q.119, L.123, R.136 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.81, C:R.84, C:Q.119 Water bridges: C:N.83, C:E.116 Salt bridges: C:K.81, C:R.136 SO4.20: 6 residues within 4Å: Chain D: G.80, K.81, N.82, R.84, Q.119, R.136 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.81, D:N.82, D:R.84, D:Q.119 Salt bridges: D:K.81, D: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

2012-05-23

Peptides

Farnesyl pyrophosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

Farnesyl pyrophosphate synthase

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