SMTL ID : 4jzb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: CA.2, P2H.5 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.2: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: CA.1, P2H.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.1 CA.3: 2 residues within 4Å: Chain A: D.250 Ligands: P2H.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.1 CA.9: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: P2H.8, CA.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.14, H2O.15 CA.10: 2 residues within 4Å: Chain B: D.250 Ligands: P2H.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.14, H2O.14, H2O.15 CA.11: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: P2H.8, CA.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.14, H2O.14, H2O.15

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

IPE.4: 12 residues within 4Å: Chain A: G.47, K.48, R.51, Q.91, R.108, T.208, Y.211, T.212, F.246, Q.247, D.250 Ligands: P2H.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.208, A:F.246, 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.7: 12 residues within 4Å: Chain B: G.47, K.48, R.51, Q.91, R.108, T.208, Y.211, T.212, F.246, Q.247, D.250 Ligands: P2H.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.208, B:F.246, B:D.250 Hydrogen bonds: B:K.48, B:R.51, B:Q.91 Water bridges: B:K.48, B:K.48, B:K.48, B:Y.49, B:Y.49, B:Y.49, B:K.264, B:K.264, B:K.264 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.108, B:K.264

2 x P2H: 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium(Non-covalent)

P2H.5: 17 residues within 4Å: Chain A: F.94, D.98, M.101, D.102, R.107, T.163, Q.167, K.207, T.208, Q.247, D.250, K.264 Chain B: N.126 Ligands: CA.1, CA.2, CA.3, IPE.4 15 PLIP interactions: 15 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:R.107, A:R.107, A:K.207, A:Q.247, A:Q.247 Water bridges: A:S.104, A:D.250, A:K.264 P2H.8: 18 residues within 4Å: Chain A: N.126 Chain B: F.94, D.98, M.101, D.102, R.107, T.163, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: IPE.7, CA.9, CA.10, CA.11 17 PLIP interactions: 17 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:R.107, B:R.107, B:K.207, B:Q.247, B:Q.247 Water bridges: B:D.102, B:S.104, B:S.104, B:D.250, B:K.264

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: G.266, E.270, V.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.266 Water bridges: A:K.309 NA.12: 3 residues within 4Å: Chain B: G.266, E.270, V.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.270 Water bridges: B:K.309

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

2014-02-12

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase

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