SMTL ID : 4nfj.1

Crystal structure of human FPPS in complex with magnesium, JDS05120, and sulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x JD5: [({5-[4-(cyclopropyloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)(Non-covalent)

JD5.1: 21 residues within 4Å: Chain A: F.120, F.121, A.124, D.125, M.128, D.129, R.134, T.189, E.190, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Chain B: N.152, N.155 Ligands: MG.2, MG.3, MG.4 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.120, A:F.121, A:F.121, A:D.125, A:T.189, A:E.190, A:Q.193, B:N.155 Hydrogen bonds: A:D.125, A:R.134, A:R.134, A:K.222, A:Y.226, A:Q.262, A:K.279 Water bridges: A:D.129, A:D.129, A:D.129, A:Q.193, A:K.288, A:K.288 JD5.6: 21 residues within 4Å: Chain A: N.152, N.155 Chain B: F.120, F.121, A.124, D.125, M.128, D.129, R.134, T.189, E.190, Q.193, K.222, T.223, Y.226, Q.262, D.265, K.279 Ligands: MG.7, MG.8, MG.9 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.120, B:F.121, B:F.121, B:D.125, B:T.189, B:E.190, B:Q.193, A:N.155 Hydrogen bonds: B:D.125, B:R.134, B:R.134, B:K.222, B:Q.262, B:K.279 Water bridges: B:Q.193, B:K.288, B:K.288

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.125, D.129, Q.193, D.196 Ligands: JD5.1, MG.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.1, H2O.1 MG.3: 2 residues within 4Å: Chain A: D.265 Ligands: JD5.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: JD5.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.1 MG.7: 6 residues within 4Å: Chain B: D.125, D.129, Q.193, D.196 Ligands: JD5.6, MG.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.5, H2O.5, H2O.5 MG.8: 2 residues within 4Å: Chain B: D.265 Ligands: JD5.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.5, H2O.5, H2O.5 MG.9: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: JD5.6, MG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.5, H2O.5

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:R.82, A:E.115, A:R.135 Salt bridges: A:R.82, A:R.135 SO4.10: 5 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:R.82, B:E.115, B:R.135 Salt bridges: B:R.82, B:R.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Crystallographic and thermodynamic characterization of phenylaminopyridine bisphosphonates binding to human farnesyl pyrophosphate synthase. PLoS ONE (2017)

Release Date

2014-12-31

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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