SMTL ID : 2ewg.2 (3 other biounits)

T. brucei Farnesyl Diphosphate Synthase Complexed with Minodronate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.126, D.130, R.135 Ligands: MG.2, M0N.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.126, A:D.130, H2O.1, H2O.7 MG.2: 5 residues within 4Å: Chain A: D.126, D.130, Q.195 Ligands: MG.1, M0N.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, A:D.126, A:D.130, A:D.130, H2O.1 MG.3: 4 residues within 4Å: Chain A: D.278, D.282, D.296 Ligands: M0N.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.278, H2O.1, H2O.1, H2O.3 MG.7: 5 residues within 4Å: Chain B: D.126, D.130, R.135 Ligands: MG.8, M0N.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.126, B:D.130, H2O.7, H2O.14 MG.8: 5 residues within 4Å: Chain B: D.126, D.130, Q.195 Ligands: MG.7, M0N.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, B:D.126, B:D.130, B:D.130, H2O.7 MG.9: 4 residues within 4Å: Chain B: D.278, D.282, D.296 Ligands: M0N.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.278, H2O.7, H2O.7, H2O.10 MG.13: 5 residues within 4Å: Chain C: D.126, D.130, S.132 Ligands: MG.15, M0N.16 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.126, C:D.130, H2O.14, H2O.14 MG.14: 4 residues within 4Å: Chain C: D.278, D.282, D.296 Ligands: M0N.16 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.278, H2O.14, H2O.20 MG.15: 5 residues within 4Å: Chain C: D.126, D.130, D.198 Ligands: MG.13, M0N.16 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.126, C:D.130, C:D.130, H2O.14, H2O.14 MG.18: 5 residues within 4Å: Chain D: D.126, D.130, S.132 Ligands: MG.20, M0N.21 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.126, D:D.130, H2O.20, H2O.20 MG.19: 4 residues within 4Å: Chain D: D.278, D.282, D.296 Ligands: M0N.21 4 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:D.278, H2O.20, H2O.26, M0N.21 MG.20: 5 residues within 4Å: Chain D: D.126, D.130, D.198 Ligands: MG.18, M0N.21 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.126, D:D.130, D:D.130, H2O.20, H2O.20

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

M0N.4: 15 residues within 4Å: Chain A: Y.122, D.126, D.130, R.135, T.191, Q.195, K.235, T.236, Y.239, Q.275, D.278, K.292 Ligands: MG.1, MG.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.122, A:D.126, A:T.191, A:Q.195, A:Y.239 Hydrogen bonds: A:D.126, A:D.130, A:R.135, A:R.135, A:K.235, A:Q.275, A:K.292 Water bridges: A:S.132, A:S.132, A:S.132, A:T.236, A:T.236, A:D.296 M0N.10: 15 residues within 4Å: Chain B: Y.122, D.126, D.130, R.135, T.191, Q.195, K.235, T.236, Y.239, Q.275, D.278, K.292 Ligands: MG.7, MG.8, MG.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.122, B:D.126, B:T.191, B:Q.195, B:Y.239 Hydrogen bonds: B:D.126, B:D.130, B:R.135, B:R.135, B:K.235, B:Y.239, B:Q.275, B:K.292 Water bridges: B:S.132, B:S.132, B:S.132, B:D.296 M0N.16: 14 residues within 4Å: Chain C: Y.122, D.126, D.130, R.135, T.191, Q.195, K.235, T.236, Q.275, D.278, K.292 Ligands: MG.13, MG.14, MG.15 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.122, C:D.126, C:T.191, C:Q.195 Hydrogen bonds: C:D.126, C:R.135, C:R.135, C:K.235, C:K.235, C:Q.275, C:Q.275, C:D.278 Water bridges: C:D.126, C:D.127, C:D.130, C:D.130, C:S.132 M0N.21: 14 residues within 4Å: Chain D: Y.122, D.126, D.130, R.135, T.191, Q.195, K.235, T.236, Q.275, D.278, K.292 Ligands: MG.18, MG.19, MG.20 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.122, D:D.126, D:T.191, D:Q.195 Hydrogen bonds: D:D.126, D:D.126, D:R.135, D:R.135, D:K.235, D:K.235, D:Q.275, D:Q.275, D:D.278 Water bridges: D:D.126, D:D.127, D:D.130, D:S.132, D:S.132

6 x PGO: S-1,2-PROPANEDIOL(Non-covalent)(Non-functional Binders)

PGO.5: 2 residues within 4Å: Chain A: R.103, R.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.99, A:R.174 PGO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGO.11: 2 residues within 4Å: Chain B: R.103, R.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.99, B:R.174 PGO.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGO.17: 1 residues within 4Å: Chain C: H.106 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.106 Water bridges: C:R.174 PGO.22: 1 residues within 4Å: Chain D: H.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.106 Water bridges: D:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mao, J. et al., Solid-state NMR, crystallographic, and computational investigation of bisphosphonates and farnesyl diphosphate synthase-bisphosphonate complexes. J.Am.Chem.Soc. (2006)

Release Date

2006-10-31

Peptides

farnesyl pyrophosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

farnesyl pyrophosphate synthase

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