SMTL ID : 8w7h.1 (3 other biounits)

Purine Nucleoside Phosphorylase in complex with MMV000848

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x XUH: (2R)-1-(9H-carbazol-9-yl)-3-(cyclopentylamino)propan-2-ol(Non-covalent)

XUH.1: 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: PO4.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.66, A:Y.160, A:V.181, A:P.209 Hydrogen bonds: A:S.91, A:D.206 pi-Stacking: A:Y.160, A:Y.160 XUH.6: 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: PO4.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.66, B:Y.160, B:V.181, B:P.209 Hydrogen bonds: B:S.91, B:D.206 pi-Stacking: B:Y.160, B:Y.160 XUH.11: 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: PO4.15 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.66, C:Y.160, C:V.181, C:P.209 Hydrogen bonds: C:S.91, C:D.206 pi-Stacking: C:Y.160, C:Y.160 XUH.16: 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: PO4.20 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.66, D:Y.160, D:V.181, D:P.209 Hydrogen bonds: D:S.91, D:D.206 pi-Stacking: D:Y.160, D:Y.160 XUH.21: 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: PO4.25 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.66, E:Y.160, E:V.181, E:P.209 Hydrogen bonds: E:S.91, E:D.206 pi-Stacking: E:Y.160, E:Y.160 XUH.26: 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: PO4.30 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.66, F:Y.160, F:V.181, F:P.209 Hydrogen bonds: F:S.91, F:D.206 pi-Stacking: F:Y.160, F:Y.160

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

EDO.2: 2 residues within 4Å: Chain A: S.37, Y.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.38 EDO.7: 2 residues within 4Å: Chain B: S.37, Y.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.38 EDO.12: 2 residues within 4Å: Chain C: S.37, Y.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.38 EDO.17: 2 residues within 4Å: Chain D: S.37, Y.38 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.38 EDO.22: 2 residues within 4Å: Chain E: S.37, Y.38 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.38 EDO.27: 2 residues within 4Å: Chain F: S.37, Y.38 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.38

12 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: E.46, V.66 Chain D: E.46, V.66 Ligands: NA.18 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.46, D:V.66, D:V.66, A:V.66 Water bridges: D:G.70, D:G.70 NA.4: 7 residues within 4Å: Chain A: S.68, A.69, D.158 Chain D: S.68, A.69, D.158 Ligands: NA.19 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.68, A:S.68, A:A.69, D:S.68, D:A.69 Water bridges: A:D.158 NA.8: 5 residues within 4Å: Chain B: E.46, V.66 Chain F: E.46, V.66 Ligands: NA.28 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:E.46, F:V.66, B:E.46, B:V.66 Water bridges: F:G.70, F:G.70 NA.9: 7 residues within 4Å: Chain B: S.68, A.69, D.158 Chain F: S.68, A.69, D.158 Ligands: NA.29 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:S.68, B:A.69, F:S.68, F:S.68, F:A.69 Water bridges: B:D.158 NA.13: 5 residues within 4Å: Chain C: E.46, V.66 Chain E: E.46, V.66 Ligands: NA.23 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:V.66, C:V.66, E:E.46, E:V.66 Water bridges: E:G.70, E:G.70 NA.14: 7 residues within 4Å: Chain C: S.68, A.69, D.158 Chain E: S.68, A.69, D.158 Ligands: NA.24 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:S.68, C:A.69, E:S.68, E:S.68, E:A.69 Water bridges: C:D.158 NA.18: 5 residues within 4Å: Chain A: E.46, V.66 Chain D: E.46, V.66 Ligands: NA.3 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.46, D:V.66, D:V.66, A:V.66 Water bridges: D:G.70, D:G.70 NA.19: 7 residues within 4Å: Chain A: S.68, A.69, D.158 Chain D: S.68, A.69, D.158 Ligands: NA.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.68, A:S.68, A:A.69, D:S.68, D:A.69 Water bridges: A:D.158 NA.23: 5 residues within 4Å: Chain C: E.46, V.66 Chain E: E.46, V.66 Ligands: NA.13 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:E.46, E:V.66, E:V.66, C:V.66 Water bridges: E:G.70, E:G.70 NA.24: 7 residues within 4Å: Chain C: S.68, A.69, D.158 Chain E: S.68, A.69, D.158 Ligands: NA.14 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:S.68, E:A.69, C:S.68, C:S.68, C:A.69 Water bridges: C:D.158 NA.28: 5 residues within 4Å: Chain B: E.46, V.66 Chain F: E.46, V.66 Ligands: NA.8 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:E.46, F:V.66, B:E.46, B:V.66 Water bridges: F:G.70, F:G.70 NA.29: 7 residues within 4Å: Chain B: S.68, A.69, D.158 Chain F: S.68, A.69, D.158 Ligands: NA.9 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:S.68, F:S.68, F:A.69, B:S.68, B:A.69 Water bridges: B:D.158

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

PO4.5: 8 residues within 4Å: Chain A: G.23, R.27, R.88, A.89, G.90, S.91 Chain D: R.45 Ligands: XUH.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.23, A:R.27, A:A.89, A:S.91, A:S.91 Water bridges: A:D.24, D:R.45 Salt bridges: A:R.88, D:R.45 PO4.10: 8 residues within 4Å: Chain B: G.23, R.27, R.88, A.89, G.90, S.91 Chain F: R.45 Ligands: XUH.6 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:G.23, B:R.27, B:A.89, B:S.91, B:S.91 Water bridges: B:D.24, F:R.45 Salt bridges: B:R.88, F:R.45 PO4.15: 8 residues within 4Å: Chain C: G.23, R.27, R.88, A.89, G.90, S.91 Chain E: R.45 Ligands: XUH.11 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:G.23, C:R.27, C:A.89, C:S.91, C:S.91 Water bridges: C:D.24, E:R.45 Salt bridges: C:R.88, E:R.45 PO4.20: 8 residues within 4Å: Chain A: R.45 Chain D: G.23, R.27, R.88, A.89, G.90, S.91 Ligands: XUH.16 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.23, D:R.27, D:A.89, D:S.91, D:S.91 Water bridges: D:D.24, A:R.45 Salt bridges: D:R.88, A:R.45 PO4.25: 8 residues within 4Å: Chain C: R.45 Chain E: G.23, R.27, R.88, A.89, G.90, S.91 Ligands: XUH.21 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.23, E:R.27, E:A.89, E:S.91, E:S.91 Water bridges: E:D.24, C:R.45 Salt bridges: E:R.88, C:R.45 PO4.30: 8 residues within 4Å: Chain B: R.45 Chain F: G.23, R.27, R.88, A.89, G.90, S.91 Ligands: XUH.26 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.23, F:R.27, F:A.89, F:S.91, F:S.91 Water bridges: F:D.24, B:R.45 Salt bridges: F:R.88, B:R.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, Z. et al., Identification and structural validation of purine nucleoside phosphorylase from Plasmodium falciparum as a target of MMV000848. J.Biol.Chem. (2023)

Release Date

2024-01-17

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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