SMTL ID : 4ga3.1

Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with BPH-1260

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x 4GA: 1-butyl-3-(2-hydroxy-2,2-diphosphonoethyl)-1H-imidazol-3-ium(Covalent)

4GA.1: 15 residues within 4Å: Chain A: F.94, L.95, D.98, D.102, R.107, Q.166, K.195, T.196, Q.235, D.238, K.252 Ligands: MG.2, MG.3, MG.4, PO4.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.94 Hydrogen bonds: A:R.107, A:R.107, A:Q.235, A:D.238 Water bridges: A:S.104, A:S.104, A:Q.166, A:D.169, A:K.195, A:K.195, A:D.238, A:K.252, A:K.252 4GA.7: 15 residues within 4Å: Chain B: F.94, L.95, D.98, D.102, R.107, Q.166, K.195, T.196, Q.235, D.238, K.252 Ligands: MG.8, MG.9, MG.10, PO4.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.94 Hydrogen bonds: B:R.107, B:R.107, B:Q.235, B:D.238 Water bridges: B:S.104, B:S.104, B:Q.166, B:D.169, B:K.195, B:K.195, B:D.239, B:D.242, B:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.238 Ligands: 4GA.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.238, H2O.1, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.98, D.102, Q.166 Ligands: 4GA.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain A: D.98, D.102, R.107 Ligands: 4GA.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain B: D.238 Ligands: 4GA.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.238, H2O.3, H2O.3, H2O.3 MG.9: 5 residues within 4Å: Chain B: D.98, D.102, Q.166 Ligands: 4GA.7, MG.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.3, H2O.3 MG.10: 5 residues within 4Å: Chain B: D.98, D.102, R.107 Ligands: 4GA.7, MG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.3, H2O.3

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 9 residues within 4Å: Chain A: R.55, Q.91, R.107, F.234, D.238, K.252, R.346 Ligands: 4GA.1, PO4.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.91, A:R.107, A:R.346 Water bridges: A:D.238 Salt bridges: A:K.52, A:R.55, A:K.252 PO4.6: 6 residues within 4Å: Chain A: G.51, K.52, R.55, Q.91, R.108 Ligands: PO4.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.52, A:Q.91 Water bridges: A:Y.53, A:R.55, A:K.348 Salt bridges: A:K.52, A:R.55, A:R.108 PO4.11: 9 residues within 4Å: Chain B: R.55, Q.91, R.107, F.234, D.238, K.252, R.346 Ligands: 4GA.7, PO4.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.91, B:R.107, B:D.238, B:R.346 Water bridges: B:D.238 Salt bridges: B:K.52, B:R.55, B:K.252 PO4.12: 6 residues within 4Å: Chain B: G.51, K.52, R.55, Q.91, R.108 Ligands: PO4.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.52, B:Q.91 Water bridges: B:Y.53, B:R.55, B:K.348 Salt bridges: B:K.52, B:R.55, B:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., Chemo-Immunotherapeutic Anti-Malarials Targeting Isoprenoid Biosynthesis. ACS MED.CHEM.LETT. (2013)

Release Date

2013-05-08

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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