SMTL ID : 4h5d.1

Crystal structure of human FPPS in ternary complex with YS0470 and inorganic pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 x YS4: [({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)(Non-covalent)

YS4.1: 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.3, MG.4, MG.5 26 PLIP interactions: 25 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.120, A:F.121, A:F.121, A:A.124, A:T.189, A:E.190, A:Q.193, A:Y.226, B:N.155 Hydrogen bonds: A:D.125, A:R.134, A:R.134, A:K.222, A:Q.262, A:K.279 Water bridges: A:D.125, A:D.129, A:D.129, A:D.129, A:S.131, A:D.196, A:Y.226, A:D.269, A:D.269, A:K.279, A:K.279 YS4.6: 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.8, MG.9, MG.10 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:A.124, B:T.189, B:E.190, B:Q.193, B:Y.226, 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:D.125, B:S.131, B:D.196, B:T.223, B:K.279, B:K.279

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 6 residues within 4Å: Chain A: G.78, K.79, R.82, Q.118, R.135, F.261 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.79, A:R.82, A:Q.118, A:R.373 Water bridges: A:K.79, A:K.79, A:Y.80, A:Y.80, A:N.81, A:R.82, A:R.134, A:R.134, A:K.279, A:K.279, A:K.279 Salt bridges: A:K.79, A:K.79, A:R.82, A:R.135 POP.7: 6 residues within 4Å: Chain B: G.78, K.79, R.82, Q.118, R.135, F.261 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.79, B:R.82, B:Q.118, B:R.373 Water bridges: B:K.79, B:K.79, B:Y.80, B:Y.80, B:N.81, B:R.82, B:R.134, B:R.134, B:K.279, B:K.279, B:K.279 Salt bridges: B:K.79, B:K.79, B:R.82, B:R.135

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.125, D.129, K.288 Ligands: YS4.1, 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.4: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: YS4.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.1, H2O.4 MG.5: 2 residues within 4Å: Chain A: D.265 Ligands: YS4.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain B: D.125, D.129, K.288 Ligands: YS4.6, MG.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.6, H2O.6, H2O.6 MG.9: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: YS4.6, MG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.6, H2O.10 MG.10: 2 residues within 4Å: Chain B: D.265 Ligands: YS4.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.6, H2O.6, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure. Bmc Struct.Biol. (2012)

Release Date

2012-12-26

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

Farnesyl pyrophosphate synthase

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