SMTL ID : 3rye.1

Human FDPS Synthase in Complex with a N-Methyl Pyridinum Bisphosphonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x UNR: 3-(2-hydroxy-2,2-diphosphonoethyl)-1-methylpyridinium(Non-covalent)

UNR.1: 16 residues within 4Å: Chain A: F.95, L.96, D.99, D.103, R.108, T.163, Q.167, K.196, T.197, Y.200, Q.236, D.239, K.253 Ligands: MG.2, MG.3, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.96, A:K.196 Hydrogen bonds: A:R.108, A:R.108, A:Q.236 Water bridges: A:S.105, A:S.105, A:Q.167, A:D.170, A:K.196, A:K.196, A:K.196, A:K.196, A:D.239, A:D.239, A:K.253 UNR.6: 16 residues within 4Å: Chain B: F.95, L.96, D.99, D.103, R.108, T.163, Q.167, K.196, T.197, Y.200, Q.236, D.239, K.253 Ligands: MG.7, MG.8, MG.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.96, B:K.196 Hydrogen bonds: B:R.108, B:R.108, B:Q.236 Water bridges: B:D.103, B:D.103, B:D.103, B:S.105, B:Q.167, B:D.170, B:K.196, B:K.196, B:K.196, B:K.196, B:T.197, B:D.243

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.99, D.103 Ligands: UNR.1, MG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.99, A:D.103, H2O.6, H2O.6 MG.3: 3 residues within 4Å: Chain A: D.239, D.243 Ligands: UNR.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.239, H2O.5, H2O.6, H2O.6 MG.4: 5 residues within 4Å: Chain A: D.99, D.103, D.170 Ligands: UNR.1, MG.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.99, A:D.103, H2O.1, H2O.4, H2O.6 MG.7: 4 residues within 4Å: Chain B: D.99, D.103 Ligands: UNR.6, MG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.99, B:D.103, H2O.12, H2O.12 MG.8: 3 residues within 4Å: Chain B: D.239, D.243 Ligands: UNR.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.239, H2O.11, H2O.12, H2O.12 MG.9: 5 residues within 4Å: Chain B: D.99, D.103, D.170 Ligands: UNR.6, MG.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.99, B:D.103, H2O.6, H2O.9, H2O.12

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

SO4.5: 5 residues within 4Å: Chain A: G.52, K.53, R.56, Q.92, R.109 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.53, A:R.56, A:Q.92 Water bridges: A:Y.54, A:Y.54, A:Y.54, A:N.55 Salt bridges: A:R.109 SO4.10: 5 residues within 4Å: Chain B: G.52, K.53, R.56, Q.92, R.109 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.53, B:R.56, B:Q.92 Water bridges: B:Y.54, B:Y.54, B:Y.54, B:N.55 Salt bridges: B:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evdokimov, A.G. et al., Human FDPS Synthase in Complex with a N-Methyl Pyridinum Bisphosphonate. To be Published

Release Date

2011-06-01

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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