SMTL ID : 4kq5.1

Crystal Structure of Human Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg and Zoledronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.125, D.129, R.134 Ligands: MG.3, ZOL.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.4, H2O.4 MG.2: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: ZOL.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.4, H2O.4, H2O.4 MG.3: 6 residues within 4Å: Chain A: D.125, D.129, D.196, K.288 Ligands: MG.1, ZOL.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.125, A:D.129, H2O.4, H2O.4, H2O.4 MG.6: 5 residues within 4Å: Chain B: D.125, D.129, R.134 Ligands: MG.8, ZOL.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.11, H2O.11 MG.7: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: ZOL.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.11, H2O.11, H2O.11 MG.8: 6 residues within 4Å: Chain B: D.125, D.129, D.196, K.288 Ligands: MG.6, ZOL.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, B:D.129, H2O.11, H2O.11, H2O.11

2 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.4: 13 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.1, MG.2, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.134, A:R.134, A:Q.262, A:D.265 Water bridges: A:D.126, A:S.131, A:K.222, A:K.222, A:D.269, A:D.269, A:D.269, A:D.269, A:D.269 pi-Cation interactions: A:K.222 ZOL.9: 13 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, Q.193, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.6, MG.7, MG.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.134, B:R.134, B:Q.262, B:D.265 Water bridges: B:D.126, B:S.131, B:K.222, B:K.222, B:D.265, B:D.269, B:D.269 pi-Cation interactions: B:K.222

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: Y.141, G.147, L.148 Chain B: L.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.141 Water bridges: A:I.127, A:G.147, A:L.148 EDO.10: 4 residues within 4Å: Chain A: L.148 Chain B: Y.141, G.147, L.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.141 Water bridges: B:I.127, B:Y.141, B:G.147, B:L.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsoumpra, M.K. et al., Crystal Structure of Human Farnesyl Pyrophosphate Synthase Mutant (Y204A) Complexed with Mg and Zoledronate. To be Published

Release Date

2014-04-30

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl pyrophosphate synthase

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