SMTL ID : 2p1c.1

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-210

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.126, D.130, S.132 Ligands: GG3.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.5, H2O.6 MG.2: 4 residues within 4Å: Chain A: D.278, D.282, D.296 Ligands: GG3.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.278, H2O.5 MG.3: 6 residues within 4Å: Chain A: D.126, D.130, Q.195, D.198, K.301 Ligands: GG3.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, A:D.130, H2O.5 MG.7: 6 residues within 4Å: Chain B: D.126, D.127, D.130, S.132, R.135 Ligands: GG3.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.12 MG.8: 4 residues within 4Å: Chain B: D.278, D.282, D.296 Ligands: GG3.11 No protein-ligand interaction detected (PLIP) MG.9: 5 residues within 4Å: Chain B: D.126, D.130, Q.195, D.198 Ligands: GG3.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.126, B:D.130

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

ACT.4: 3 residues within 4Å: Chain A: Q.119, R.136 Ligands: ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.119 Salt bridges: A:R.73, A:R.136 ACT.5: 5 residues within 4Å: Chain A: G.69, K.70, Y.71, N.72 Ligands: ACT.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.70 Hydrogen bonds: A:K.70, A:Y.71, A:N.72, A:N.72 Water bridges: A:R.73 ACT.10: 3 residues within 4Å: Chain B: R.73, Q.119, R.136 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.136 Hydrogen bonds: B:Q.119 Water bridges: B:K.70, B:Y.71, B:N.72, B:R.73, B:R.73 Salt bridges: B:R.73, B:R.136

2 x GG3: {1-HYDROXY-3-[METHYL(4-PHENYLBUTYL)AMINO]PROPANE-1,1-DIYL}BIS(PHOSPHONIC ACID)(Non-covalent)

GG3.6: 20 residues within 4Å: Chain A: Y.122, L.123, D.126, M.129, D.130, R.135, T.191, A.192, Q.195, K.235, T.236, Y.239, Q.275, D.278, K.292 Chain B: N.154, L.157 Ligands: MG.1, MG.2, MG.3 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.122, A:Y.122, A:Y.122, A:Q.195, A:Y.239, B:L.157 Hydrogen bonds: A:R.135, A:R.135, A:K.235, A:Q.275, A:K.292 Water bridges: A:S.132 Salt bridges: A:D.126 GG3.11: 20 residues within 4Å: Chain A: N.154, L.157 Chain B: Y.122, L.123, E.125, D.126, D.130, R.135, T.191, A.192, Q.195, K.235, T.236, Y.239, Q.275, D.278, K.292 Ligands: MG.7, MG.8, MG.9 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.122, B:Y.122, B:E.125, B:T.191, B:Q.195, A:L.157 Hydrogen bonds: B:R.135, B:R.135, B:K.235, B:Y.239, B:Q.275 Water bridges: B:D.130, B:S.132, B:D.278, B:K.292, B:D.296

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.12: 4 residues within 4Å: Chain B: D.179, C.182, R.183, R.186 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, R. et al., Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases. Proteins (2008)

Release Date

2008-03-04

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase

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