SMTL ID : 3zou.1

Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment SPB02696, and substrate geranyl pyrophosphate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.84, D.90, Q.158 Ligands: MG.2, GPP.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.84, A:D.90, H2O.5, H2O.5, H2O.5 MG.2: 4 residues within 4Å: Chain A: D.84, D.90 Ligands: MG.1, GPP.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.84, A:D.90, H2O.5, H2O.5 MG.4: 1 residues within 4Å: Chain A: D.224 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.224, H2O.9, H2O.10, H2O.10, H2O.10, H2O.12 MG.7: 2 residues within 4Å: Chain B: D.92, L.94 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.92, B:L.94, H2O.17, H2O.17, H2O.17, H2O.17 MG.8: 3 residues within 4Å: Chain B: D.84, D.90, D.92 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.92, H2O.16, H2O.16, H2O.17 MG.9: 1 residues within 4Å: Chain B: D.224 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.224, H2O.20, H2O.21, H2O.21, H2O.21, H2O.22 MG.13: 2 residues within 4Å: Chain B: D.84, D.90 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.84, B:D.84, H2O.16, H2O.17, H2O.22

1 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.3: 13 residues within 4Å: Chain A: S.80, L.81, H.83, D.84, D.90, R.95, V.155, Q.158, K.181, T.182 Chain B: L.112 Ligands: MG.1, MG.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.83, A:D.84, A:V.155, A:Q.158, A:K.181, A:T.182, B:L.112 Water bridges: A:R.95, A:Q.158, A:D.161, A:D.161, A:K.181 Salt bridges: A:R.95, A:K.181

2 x 6H6: 3-(2-oxo-1,3-benzoxazol-3(2H)-yl)propanoic acid(Non-covalent)

6H6.5: 8 residues within 4Å: Chain A: I.3, A.4, Q.7, K.45, V.47, L.50, L.287, Y.290 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.7, A:V.47, A:L.50, A:L.287 Hydrogen bonds: A:Q.7 Salt bridges: A:K.45 pi-Stacking: A:Y.290 6H6.6: 8 residues within 4Å: Chain B: I.3, A.4, Q.7, K.45, V.47, L.50, L.287, Y.290 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Q.7, B:V.47, B:L.50, B:L.287 Water bridges: B:Q.7, B:Q.11 Salt bridges: B:K.45 pi-Stacking: B:Y.290

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain B: Y.6, R.9, C.10, R.13, E.57, P.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.6 GOL.12: 6 residues within 4Å: Chain B: L.21, L.120, E.123, V.124, D.127, R.130 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.127, B:D.127, B:R.130 Water bridges: B:L.21

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 6 residues within 4Å: Chain B: S.80, L.81, D.84, M.154, Q.158, K.181 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidberger, J.W. et al., Structural Characterization of Substrate and Inhibitor Binding to Farnesyl Pyrophosphate Synthase from Pseudomonas Aeruginosa. Acta Crystallogr.,Sect.D (2015)

Release Date

2014-03-12

Peptides

FARNESYL PYROPHOSPHATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FARNESYL PYROPHOSPHATE SYNTHASE

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