SMTL ID : 4nfk.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: NI.3, JD5.4 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 NI.2: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: JD5.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.1 NI.3: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: NI.1, JD5.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.1 NI.6: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: NI.8, JD5.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.10, H2O.10, H2O.10 NI.7: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: JD5.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.10, H2O.10, H2O.10 NI.8: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: NI.6, JD5.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.10, H2O.10

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

JD5.4: 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: NI.1, NI.2, NI.3 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:F.121, A:A.124, A:D.125, A:T.189, 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:Q.118, A:S.131, A:S.131, A:S.131, A:D.269 JD5.9: 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: NI.6, NI.7, NI.8 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.120, B:F.121, B:F.121, B:F.121, B:A.124, B:D.125, B:T.189, 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.118, B:S.131, B:S.131, B:S.131, B:Q.193, B:Y.226

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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.79, A:Q.118 Water bridges: A:Y.80, A:Y.80, A:R.82, A:R.82, A:R.82, 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 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.79, B:Q.118 Water bridges: B:Y.80, B:Y.80, B:Y.80, B:R.82, B:R.82, B:R.82 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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