SMTL ID : 4kpj.1

Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 210: PAMIDRONATE(Non-covalent)

210.1: 13 residues within 4Å: Chain A: L.122, D.125, D.129, R.134, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.2, MG.3, MG.4, EDO.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.122 Hydrogen bonds: A:R.134, A:R.134, A:K.222, A:Q.262, A:Q.262, A:D.265, A:K.279 Water bridges: A:Q.118, A:D.129, A:D.129, A:S.131, A:S.131, A:S.131, A:Q.193, A:D.269, A:D.269 210.11: 13 residues within 4Å: Chain B: L.122, D.125, D.129, R.134, K.222, T.223, Q.262, D.265, K.279 Ligands: MG.12, MG.13, MG.14, EDO.16 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.122 Hydrogen bonds: B:R.134, B:R.134, B:K.222, B:Q.262, B:Q.262, B:D.265, B:K.279 Water bridges: B:Q.118, B:S.131, B:S.131, B:S.131, B:S.131, B:Q.193, B:D.265, B:D.265

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.125, D.129 Ligands: 210.1, MG.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 MG.3: 3 residues within 4Å: Chain A: D.265, D.269 Ligands: 210.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.265, H2O.1, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain A: D.125, D.129, D.196 Ligands: 210.1, MG.2 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.12: 4 residues within 4Å: Chain B: D.125, D.129 Ligands: 210.11, MG.14 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.13: 3 residues within 4Å: Chain B: D.265, D.269 Ligands: 210.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.265, H2O.11, H2O.11, H2O.11 MG.14: 5 residues within 4Å: Chain B: D.125, D.129, D.196 Ligands: 210.11, MG.12 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

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

EDO.5: 9 residues within 4Å: Chain A: D.269, L.270, D.283, I.284, S.290, L.292, V.293, Y.312, Y.327 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.290, A:V.293, A:Y.312, A:Y.312 Water bridges: A:I.284 EDO.6: 8 residues within 4Å: Chain A: Q.118, F.121, T.189, K.222, T.223, A.226, S.227 Ligands: 210.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.118, A:S.227 Water bridges: A:R.82, A:T.189, A:A.226 EDO.7: 5 residues within 4Å: Chain A: P.173, Y.174, Y.175, L.176, N.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.173, A:L.176, A:N.177 Water bridges: A:Y.175 EDO.8: 8 residues within 4Å: Chain A: L.268, D.269, G.272, P.274, T.277, K.279, I.280, G.281 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.277, A:T.277, A:G.281 Water bridges: A:D.269, A:L.270 EDO.9: 2 residues within 4Å: Chain A: V.320, A.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.320 EDO.10: 4 residues within 4Å: Chain A: Q.304, I.307, R.322, E.329 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.304, A:R.322 Water bridges: A:R.322 EDO.15: 9 residues within 4Å: Chain B: D.269, L.270, D.283, I.284, S.290, L.292, V.293, Y.312, Y.327 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.269, B:S.290, B:V.293, B:Y.312, B:Y.327 Water bridges: B:I.284 EDO.16: 8 residues within 4Å: Chain B: Q.118, F.121, T.189, K.222, T.223, A.226, S.227 Ligands: 210.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.118, B:S.227 Water bridges: B:R.82, B:T.189, B:A.226 EDO.17: 5 residues within 4Å: Chain B: P.173, Y.174, Y.175, L.176, N.177 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.173, B:L.176, B:N.177 Water bridges: B:Y.175 EDO.18: 8 residues within 4Å: Chain B: L.268, D.269, G.272, P.274, T.277, K.279, I.280, G.281 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.277, B:G.281 Water bridges: B:D.269, B:L.270 EDO.19: 2 residues within 4Å: Chain B: V.320, A.321 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.320 EDO.20: 4 residues within 4Å: Chain B: Q.304, I.307, R.322, E.329 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.304, B:R.322 Water bridges: B:R.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsoumpra, M.K. et al., Crystal Structure of Farnesyl Pyrophosphate Synthase (Y204A) Mutant complexed with Mg, Pamidronate. 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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