SMTL ID : 5znc.1

Plasmodium falciparum purine nucleoside phosphorylase in complex with quinine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-hexamer

Ligands

6 x QI9: Quinine(Non-covalent)

QI9.1: 16 residues within 4Å: Chain A: V.66, S.91, C.92, G.93, S.157, M.159, Y.160, V.181, E.182, M.183, D.206, W.212, D.218 Chain F: H.7, R.45 Ligands: PO4.2 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:V.66, A:V.181, A:W.212, A:D.218, F:H.7 Water bridges: A:S.91, A:M.183 Salt bridges: A:D.218 pi-Stacking: A:Y.160 QI9.5: 16 residues within 4Å: Chain B: V.66, S.91, C.92, G.93, S.157, M.159, Y.160, V.181, E.182, M.183, D.206, W.212, D.218 Chain E: H.7, R.45 Ligands: PO4.6 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:V.66, B:V.181, B:W.212, B:D.218, E:H.7 Water bridges: B:S.91, B:M.183 Salt bridges: B:D.218 pi-Stacking: B:Y.160 QI9.9: 16 residues within 4Å: Chain C: V.66, S.91, C.92, G.93, S.157, M.159, Y.160, V.181, E.182, M.183, D.206, W.212, D.218 Chain D: H.7, R.45 Ligands: PO4.10 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.66, C:V.181, C:W.212, C:D.218, D:H.7 Water bridges: C:S.91, C:M.183 Salt bridges: C:D.218 pi-Stacking: C:Y.160 QI9.13: 16 residues within 4Å: Chain C: H.7, R.45 Chain D: V.66, S.91, C.92, G.93, S.157, M.159, Y.160, V.181, E.182, M.183, D.206, W.212, D.218 Ligands: PO4.14 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.66, D:V.181, D:W.212, D:D.218, C:H.7 Water bridges: D:S.91, D:M.183 Salt bridges: D:D.218 pi-Stacking: D:Y.160 QI9.17: 16 residues within 4Å: Chain B: H.7, R.45 Chain E: V.66, S.91, C.92, G.93, S.157, M.159, Y.160, V.181, E.182, M.183, D.206, W.212, D.218 Ligands: PO4.18 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:V.66, E:V.181, E:W.212, E:D.218, B:H.7 Water bridges: E:S.91, E:M.183 Salt bridges: E:D.218 pi-Stacking: E:Y.160 QI9.21: 16 residues within 4Å: Chain A: H.7, R.45 Chain F: V.66, S.91, C.92, G.93, S.157, M.159, Y.160, V.181, E.182, M.183, D.206, W.212, D.218 Ligands: PO4.22 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:V.66, F:V.181, F:W.212, F:D.218, A:H.7 Water bridges: F:S.91, F:M.183 Salt bridges: F:D.218 pi-Stacking: F:Y.160

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

PO4.2: 7 residues within 4Å: Chain A: G.23, R.88, A.89, G.90, S.91 Chain F: R.45 Ligands: QI9.1 Ligand excluded by PLIP PO4.3: 3 residues within 4Å: Chain A: H.119, H.123, G.124 Ligand excluded by PLIP PO4.4: 4 residues within 4Å: Chain A: H.7, K.9, N.44, R.45 Ligand excluded by PLIP PO4.6: 7 residues within 4Å: Chain B: G.23, R.88, A.89, G.90, S.91 Chain E: R.45 Ligands: QI9.5 Ligand excluded by PLIP PO4.7: 3 residues within 4Å: Chain B: H.119, H.123, G.124 Ligand excluded by PLIP PO4.8: 4 residues within 4Å: Chain B: H.7, K.9, N.44, R.45 Ligand excluded by PLIP PO4.10: 7 residues within 4Å: Chain C: G.23, R.88, A.89, G.90, S.91 Chain D: R.45 Ligands: QI9.9 Ligand excluded by PLIP PO4.11: 3 residues within 4Å: Chain C: H.119, H.123, G.124 Ligand excluded by PLIP PO4.12: 4 residues within 4Å: Chain C: H.7, K.9, N.44, R.45 Ligand excluded by PLIP PO4.14: 7 residues within 4Å: Chain C: R.45 Chain D: G.23, R.88, A.89, G.90, S.91 Ligands: QI9.13 Ligand excluded by PLIP PO4.15: 3 residues within 4Å: Chain D: H.119, H.123, G.124 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain D: H.7, K.9, N.44, R.45 Ligand excluded by PLIP PO4.18: 7 residues within 4Å: Chain B: R.45 Chain E: G.23, R.88, A.89, G.90, S.91 Ligands: QI9.17 Ligand excluded by PLIP PO4.19: 3 residues within 4Å: Chain E: H.119, H.123, G.124 Ligand excluded by PLIP PO4.20: 4 residues within 4Å: Chain E: H.7, K.9, N.44, R.45 Ligand excluded by PLIP PO4.22: 7 residues within 4Å: Chain A: R.45 Chain F: G.23, R.88, A.89, G.90, S.91 Ligands: QI9.21 Ligand excluded by PLIP PO4.23: 3 residues within 4Å: Chain F: H.119, H.123, G.124 Ligand excluded by PLIP PO4.24: 4 residues within 4Å: Chain F: H.7, K.9, N.44, R.45 Ligand excluded by PLIP

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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