SMTL ID : 5zni.1

Plasmodium falciparum purine nucleoside phosphorylase in complex with mefloquine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 10 residues within 4Å: Chain A: G.23, D.24, R.27, R.88, A.89, G.90, S.91, E.184 Chain D: R.45 Ligands: YMZ.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.23, A:D.24, A:S.91 Water bridges: A:R.27, A:R.27, A:R.88, A:R.88, A:R.88, A:E.184, D:R.45 Salt bridges: A:R.27, A:R.88, D:R.45 PO4.3: 10 residues within 4Å: Chain B: G.23, D.24, R.27, R.88, A.89, G.90, S.91, E.184 Chain F: R.45 Ligands: YMZ.4 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain B Water bridges: F:R.45, B:R.27, B:R.27, B:R.88, B:R.88, B:R.88, B:E.184 Salt bridges: F:R.45, B:R.27, B:R.88 Hydrogen bonds: B:G.23, B:D.24, B:S.91 PO4.5: 10 residues within 4Å: Chain C: G.23, D.24, R.27, R.88, A.89, G.90, S.91, E.184 Chain E: R.45 Ligands: YMZ.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:G.23, C:D.24, C:S.91 Water bridges: C:R.27, C:R.27, C:R.88, C:R.88, C:R.88, C:E.184, E:R.45 Salt bridges: C:R.27, C:R.88, E:R.45 PO4.7: 10 residues within 4Å: Chain A: R.45 Chain D: G.23, D.24, R.27, R.88, A.89, G.90, S.91, E.184 Ligands: YMZ.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.23, D:D.24, D:S.91 Water bridges: D:R.27, D:R.27, D:R.88, D:R.88, D:R.88, D:E.184, A:R.45 Salt bridges: D:R.27, D:R.88, A:R.45 PO4.9: 10 residues within 4Å: Chain C: R.45 Chain E: G.23, D.24, R.27, R.88, A.89, G.90, S.91, E.184 Ligands: YMZ.10 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.23, E:D.24, E:S.91 Water bridges: E:R.27, E:R.27, E:R.88, E:R.88, E:R.88, E:E.184, C:R.45 Salt bridges: E:R.27, E:R.88, C:R.45 PO4.11: 10 residues within 4Å: Chain B: R.45 Chain F: G.23, D.24, R.27, R.88, A.89, G.90, S.91, E.184 Ligands: YMZ.12 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.23, F:D.24, F:S.91 Water bridges: F:R.27, F:R.27, F:R.88, F:R.88, F:R.88, F:E.184, B:R.45 Salt bridges: F:R.27, F:R.88, B:R.45

6 x YMZ: (11R,12S)- Mefloquine(Non-covalent)

YMZ.2: 16 residues within 4Å: Chain A: V.66, S.91, C.92, G.93, M.159, Y.160, V.181, E.182, M.183, D.206, G.207, C.208, P.209 Chain D: H.7, R.45 Ligands: PO4.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.66, A:Y.160, A:D.206 Hydrogen bonds: A:M.183 Water bridges: A:E.184, A:E.184, A:E.184 pi-Stacking: A:Y.160 Halogen bonds: A:Y.160 YMZ.4: 16 residues within 4Å: Chain B: V.66, S.91, C.92, G.93, M.159, Y.160, V.181, E.182, M.183, D.206, G.207, C.208, P.209 Chain F: H.7, R.45 Ligands: PO4.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.66, B:Y.160, B:D.206 Hydrogen bonds: B:M.183 Water bridges: B:E.184, B:E.184, B:E.184 pi-Stacking: B:Y.160 Halogen bonds: B:Y.160 YMZ.6: 16 residues within 4Å: Chain C: V.66, S.91, C.92, G.93, M.159, Y.160, V.181, E.182, M.183, D.206, G.207, C.208, P.209 Chain E: H.7, R.45 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.66, C:Y.160, C:D.206 Hydrogen bonds: C:M.183 Water bridges: C:E.184, C:E.184, C:E.184 pi-Stacking: C:Y.160 Halogen bonds: C:Y.160 YMZ.8: 16 residues within 4Å: Chain A: H.7, R.45 Chain D: V.66, S.91, C.92, G.93, M.159, Y.160, V.181, E.182, M.183, D.206, G.207, C.208, P.209 Ligands: PO4.7 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.66, D:Y.160, D:D.206 Hydrogen bonds: D:M.183 Water bridges: D:E.184, D:E.184, D:E.184 pi-Stacking: D:Y.160 Halogen bonds: D:Y.160 YMZ.10: 16 residues within 4Å: Chain C: H.7, R.45 Chain E: V.66, S.91, C.92, G.93, M.159, Y.160, V.181, E.182, M.183, D.206, G.207, C.208, P.209 Ligands: PO4.9 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.66, E:Y.160, E:D.206 Hydrogen bonds: E:M.183 Water bridges: E:E.184, E:E.184, E:E.184 pi-Stacking: E:Y.160 Halogen bonds: E:Y.160 YMZ.12: 16 residues within 4Å: Chain B: H.7, R.45 Chain F: V.66, S.91, C.92, G.93, M.159, Y.160, V.181, E.182, M.183, D.206, G.207, C.208, P.209 Ligands: PO4.11 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:V.66, F:Y.160, F:D.206 Hydrogen bonds: F:M.183 Water bridges: F:E.184, F:E.184, F:E.184 pi-Stacking: F:Y.160 Halogen bonds: F:Y.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dziekan, J.M. et al., Identifying purine nucleoside phosphorylase as the target of quinine using cellular thermal shift assay. Sci Transl Med (2019)

Release Date

2019-01-16

Peptides

Purine nucleoside phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Purine nucleoside phosphorylase

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