SMTL ID : 4dxj.2 (1 other biounit)

Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-propylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.98, D.102, D.170 Ligands: MG.2, 0M9.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.2, H2O.2, H2O.2 MG.2: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: MG.1, 0M9.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.2, H2O.2 MG.3: 2 residues within 4Å: Chain A: D.250 Ligands: 0M9.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.2, H2O.2, H2O.2 MG.9: 5 residues within 4Å: Chain B: D.98, D.102, D.170 Ligands: MG.10, 0M9.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.4, H2O.4, H2O.4 MG.10: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: MG.9, 0M9.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.4, H2O.4 MG.11: 2 residues within 4Å: Chain B: D.250 Ligands: 0M9.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.3, H2O.3, H2O.4

2 x 0M9: [2-(propylamino)ethane-1,1-diyl]bis(phosphonic acid)(Non-covalent)

0M9.4: 15 residues within 4Å: Chain A: Y.94, D.98, D.102, R.107, T.163, Q.167, K.207, Y.211, Q.247, D.250, K.264 Ligands: MG.1, MG.2, MG.3, IPE.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.94, A:T.163, A:Q.167, A:Y.211 Hydrogen bonds: A:D.98, A:R.107, A:R.107, A:K.207, A:Q.247, A:K.264 Water bridges: A:S.104, A:S.104, A:S.104, A:Q.167, A:Q.167, A:D.254, A:D.254 0M9.12: 15 residues within 4Å: Chain B: Y.94, D.98, D.102, R.107, T.163, Q.167, K.207, Y.211, Q.247, D.250, K.264 Ligands: MG.9, MG.10, MG.11, IPE.13 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.94, B:T.163, B:Q.167, B:Y.211 Hydrogen bonds: B:D.98, B:R.107, B:R.107, B:K.207, B:Q.247, B:K.264 Water bridges: B:D.102, B:D.102, B:S.104, B:S.104, B:S.104, B:Q.167, B:Q.167, B:K.264

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

IPE.5: 11 residues within 4Å: Chain A: G.47, K.48, R.51, Q.91, R.108, Y.211, F.246, Q.247, D.250, K.362 Ligands: 0M9.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.246, A:D.250 Hydrogen bonds: A:K.48, A:Q.91 Water bridges: A:R.51, A:R.51, A:R.108, A:K.362 Salt bridges: A:K.48, A:K.48, A:R.51, A:R.51, A:R.108, A:K.362, A:K.362 IPE.13: 11 residues within 4Å: Chain B: G.47, K.48, R.51, Q.91, R.108, Y.211, F.246, Q.247, D.250, K.362 Ligands: 0M9.12 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.246, B:D.250 Hydrogen bonds: B:K.48, B:Q.91 Water bridges: B:R.51, B:R.51, B:R.108, B:K.362 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.51, B:R.108, B:K.362, B:K.362

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 2 residues within 4Å: Chain A: K.25, H.141 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.158, A:K.25, A:H.141 ACT.14: 2 residues within 4Å: Chain B: K.25, H.141 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.158, B:K.25, B:H.141

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 5 residues within 4Å: Chain A: L.155, F.210, L.214, M.232, E.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.236 PEG.8: 3 residues within 4Å: Chain A: L.8, D.12, D.41 No protein-ligand interaction detected (PLIP) PEG.15: 5 residues within 4Å: Chain B: L.155, F.210, L.214, M.232, E.236 No protein-ligand interaction detected (PLIP) PEG.16: 3 residues within 4Å: Chain B: L.8, D.12, D.41 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aripirala, S. et al., Design, synthesis, calorimetry, and crystallographic analysis of 2-alkylaminoethyl-1,1-bisphosphonates as inhibitors of Trypanosoma cruzi farnesyl diphosphate synthase. J.Med.Chem. (2012)

Release Date

2013-01-16

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Farnesyl pyrophosphate synthase

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