SMTL ID : 2vf6.1

Human FDPS synthase in complex with minodronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x M0N: (1-HYDROXY-2-IMIDAZO[1,2-A]PYRIDIN-3-YLETHANE-1,1-DIYL)BIS(PHOSPHONIC ACID)(Non-covalent)

M0N.1: 16 residues within 4Å: Chain A: F.124, L.125, D.128, D.132, R.137, T.192, Q.196, K.225, T.226, Y.229, Q.265, D.268, K.282 Ligands: MG.2, MG.3, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:F.124, A:L.125, A:D.128, A:T.192, A:Q.196, A:Y.229 Hydrogen bonds: A:D.128, A:D.128, A:R.137, A:R.137, A:Q.265, A:Q.265, A:K.282 Water bridges: A:S.134, A:S.134, A:S.134, A:Q.196, A:K.225, A:K.225, A:K.225, A:K.225, A:D.268, A:D.268, A:D.286, A:D.286 M0N.5: 16 residues within 4Å: Chain B: F.124, L.125, D.128, D.132, R.137, T.192, Q.196, K.225, T.226, Y.229, Q.265, D.268, K.282 Ligands: MG.6, MG.7, MG.8 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:F.124, B:L.125, B:D.128, B:T.192, B:Q.196, B:Y.229 Hydrogen bonds: B:D.128, B:D.128, B:R.137, B:R.137, B:Y.229, B:Q.265, B:Q.265, B:K.282 Water bridges: B:D.132, B:D.132, B:S.134, B:S.134, B:Q.196, B:K.225, B:K.225, B:K.225, B:K.225, B:T.226, B:D.272, B:D.272, B:D.286, B:D.286

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.268, K.282 Ligands: M0N.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.268, H2O.5, H2O.5, H2O.5 MG.3: 4 residues within 4Å: Chain A: D.128, D.132 Ligands: M0N.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.128, A:D.132, H2O.2, H2O.2 MG.4: 6 residues within 4Å: Chain A: D.128, D.132, Q.196, D.199 Ligands: M0N.1, MG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.128, A:D.132, H2O.2, H2O.7, H2O.7 MG.6: 3 residues within 4Å: Chain B: D.268, K.282 Ligands: M0N.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.268, H2O.12, H2O.12, H2O.12 MG.7: 4 residues within 4Å: Chain B: D.128, D.132 Ligands: M0N.5, MG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.128, B:D.132, H2O.9, H2O.9 MG.8: 6 residues within 4Å: Chain B: D.128, D.132, Q.196, D.199 Ligands: M0N.5, MG.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.128, B:D.132, H2O.9, H2O.14, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evdokimov, A.G. et al., Human Fdps Synthase in Complex with Novel Inhibitor. To be Published

Release Date

2007-11-06

Peptides

FARNESYL PYROPHOSPHATE SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

FARNESYL PYROPHOSPHATE SYNTHETASE

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