SMTL ID : 4k10.2 (1 other biounit)

Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 5 residues within 4Å: Chain A: R.25, H.141, A.144 Chain B: R.154, D.158 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.154, A:R.25 Water bridges: A:R.25

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

ACT.2: 5 residues within 4Å: Chain A: M.1, A.2, H.3, E.60, K.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60 Salt bridges: A:H.3, A:K.64

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.250 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: D.98, D.102, D.170 Ligands: NI9.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.2, H2O.3 MG.8: 2 residues within 4Å: Chain B: D.250 Ligands: NI9.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.250, H2O.3, H2O.3, H2O.5, H2O.5 MG.9: 3 residues within 4Å: Chain B: D.98, D.102 Ligands: NI9.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.98, B:D.98, B:D.102, H2O.5

2 x NI9: 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM(Non-covalent)

NI9.5: 9 residues within 4Å: Chain A: F.94, L.95, D.98, D.102, R.107, Q.167, K.207, Y.211 Ligands: MG.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.211 Hydrogen bonds: A:R.107, A:R.107, A:K.207 Water bridges: A:D.98, A:Q.167 pi-Cation interactions: A:K.207 NI9.10: 11 residues within 4Å: Chain B: F.94, L.95, D.98, D.102, R.107, Q.167, K.207, Y.211, K.273 Ligands: MG.8, MG.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.94 Hydrogen bonds: B:R.107, B:R.107, B:K.207, B:K.207, B:K.207

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

NA.6: 3 residues within 4Å: Chain A: A.133 Chain B: H.157, D.160 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.160 NA.7: 1 residues within 4Å: Chain B: R.25 No protein-ligand interaction detected (PLIP)

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

2014-04-02

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

Farnesyl pyrophosphate synthase

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