SMTL ID : 4jzx.1

Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 3-BUTYL-1-(2,2-DIPHOSPHONOETHYL)PYRIDINIUM, IPP and Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

IPE.1: 12 residues within 4Å: Chain A: G.47, K.48, R.51, Q.91, L.95, R.108, T.208, Y.211, F.246, Q.247, D.250 Ligands: 476.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.95, A:T.208, A:D.250 Hydrogen bonds: A:K.48, A:R.51 Water bridges: A:K.48, A:K.48, A:K.48, A:Y.49, A:Y.49, A:Y.49, A:K.264, A:K.264 Salt bridges: A:K.48, A:K.48, A:R.51, A:R.108, A:K.264 IPE.6: 12 residues within 4Å: Chain B: G.47, K.48, R.51, Q.91, L.95, R.108, T.208, Y.211, F.246, Q.247, D.250 Ligands: 476.7 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.95, B:T.208 Hydrogen bonds: B:K.48, B:R.51, B:Q.91 Water bridges: B:K.48, B:K.48, B:Y.49, B:K.264, B:K.264 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.108

2 x 476: 3-butyl-1-(2,2-diphosphonoethyl)pyridinium(Non-covalent)

476.2: 18 residues within 4Å: Chain A: F.94, D.98, D.102, R.107, T.163, T.164, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Chain B: N.126 Ligands: IPE.1, CA.3, CA.4, CA.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.94, A:F.94, A:D.98, A:T.163, A:Q.167, A:Q.167, A:K.207 Hydrogen bonds: A:D.98, A:R.107, A:R.107, A:K.207, A:Q.247 Water bridges: A:D.99, A:S.104, A:S.104, A:D.250, A:K.264 476.7: 18 residues within 4Å: Chain A: N.126 Chain B: F.94, D.98, D.102, R.107, T.163, T.164, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: IPE.6, CA.8, CA.9, CA.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.94, B:F.94, B:D.98, B:T.163, B:Q.167, B:Q.167, B:K.207 Hydrogen bonds: B:D.98, B:R.107, B:R.107, B:K.207, B:Q.247 Water bridges: B:S.104, B:S.104, B:D.250, B:K.264

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: 476.2, CA.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.1, H2O.2 CA.4: 2 residues within 4Å: Chain A: D.250 Ligands: 476.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.2 CA.5: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: 476.2, CA.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 CA.8: 5 residues within 4Å: Chain B: D.98, D.102, D.170 Ligands: 476.7, CA.10 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.16, H2O.16, H2O.17 CA.9: 2 residues within 4Å: Chain B: D.250 Ligands: 476.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.16, H2O.16, H2O.17 CA.10: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: 476.7, CA.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.16, H2O.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aripirala, S. et al., Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-03-05

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase

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