SMTL ID : 6aqs.1

Crystal structure of Plasmodium falciparum purine nucleoside phosphorylase (V181D) mutant complexed with DADMe-ImmG and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: G.24, R.28, R.89, A.90, G.91, S.92 Chain D: R.46 Ligands: IM5.2 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.24, A:S.92, A:S.92 Salt bridges: A:R.28, A:R.89, D:R.46 Water bridges: D:R.46, D:R.46 PO4.5: 8 residues within 4Å: Chain B: G.24, R.28, R.89, A.90, G.91, S.92 Chain F: R.46 Ligands: IM5.6 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:G.24, B:S.92, B:S.92 Salt bridges: B:R.28, B:R.89, F:R.46 Water bridges: F:R.46, F:R.46 PO4.9: 8 residues within 4Å: Chain C: G.24, R.28, R.89, A.90, G.91, S.92 Chain E: R.46 Ligands: IM5.10 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain C Water bridges: E:R.46, E:R.46 Salt bridges: E:R.46, C:R.28, C:R.89 Hydrogen bonds: C:G.24, C:S.92, C:S.92 PO4.13: 8 residues within 4Å: Chain A: R.46 Chain D: G.24, R.28, R.89, A.90, G.91, S.92 Ligands: IM5.14 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:G.24, D:S.92, D:S.92 Salt bridges: D:R.28, D:R.89, A:R.46 Water bridges: A:R.46, A:R.46 PO4.17: 8 residues within 4Å: Chain C: R.46 Chain E: G.24, R.28, R.89, A.90, G.91, S.92 Ligands: IM5.18 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:G.24, E:S.92, E:S.92 Salt bridges: E:R.28, E:R.89, C:R.46 Water bridges: C:R.46, C:R.46 PO4.21: 8 residues within 4Å: Chain B: R.46 Chain F: G.24, R.28, R.89, A.90, G.91, S.92 Ligands: IM5.22 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain F Water bridges: B:R.46, B:R.46 Salt bridges: B:R.46, F:R.28, F:R.89 Hydrogen bonds: F:G.24, F:S.92, F:S.92

6 x IM5: 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

IM5.2: 13 residues within 4Å: Chain A: V.67, S.92, C.93, G.94, Y.161, D.182, E.183, M.184, E.185, D.207 Chain D: H.8, R.46 Ligands: PO4.1 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:H.8, A:E.183, A:E.185, A:D.207 Water bridges: A:D.182, A:D.182, A:D.182 Salt bridges: A:D.182, A:E.185 IM5.6: 13 residues within 4Å: Chain B: V.67, S.92, C.93, G.94, Y.161, D.182, E.183, M.184, E.185, D.207 Chain F: H.8, R.46 Ligands: PO4.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:E.183, B:E.185, B:D.207, F:H.8 Water bridges: B:D.182, B:D.182, B:D.182 Salt bridges: B:D.182, B:E.185 IM5.10: 13 residues within 4Å: Chain C: V.67, S.92, C.93, G.94, Y.161, D.182, E.183, M.184, E.185, D.207 Chain E: H.8, R.46 Ligands: PO4.9 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:E.183, C:E.185, C:D.207, E:H.8 Water bridges: C:D.182, C:D.182, C:D.182 Salt bridges: C:D.182, C:E.185 IM5.14: 13 residues within 4Å: Chain A: H.8, R.46 Chain D: V.67, S.92, C.93, G.94, Y.161, D.182, E.183, M.184, E.185, D.207 Ligands: PO4.13 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:E.183, D:E.185, D:D.207, A:H.8 Water bridges: D:M.160, D:Y.161, D:D.182, D:D.182 Salt bridges: D:D.182, D:E.185 IM5.18: 13 residues within 4Å: Chain C: H.8, R.46 Chain E: V.67, S.92, C.93, G.94, Y.161, D.182, E.183, M.184, E.185, D.207 Ligands: PO4.17 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:E.183, E:E.185, E:D.207, C:H.8 Water bridges: E:M.160, E:Y.161, E:D.182, E:D.182 Salt bridges: E:D.182, E:E.185 IM5.22: 13 residues within 4Å: Chain B: H.8, R.46 Chain F: V.67, S.92, C.93, G.94, Y.161, D.182, E.183, M.184, E.185, D.207 Ligands: PO4.21 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:E.183, F:E.185, F:D.207, B:H.8 Water bridges: F:M.160, F:Y.161, F:D.182, F:D.182 Salt bridges: F:D.182, F:E.185

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

EDO.3: 3 residues within 4Å: Chain A: H.120, G.125 Ligands: EDO.4 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Water bridges: F:R.170, F:R.170 Hydrogen bonds: A:G.125 EDO.4: 5 residues within 4Å: Chain A: R.117, H.120 Chain D: R.117 Ligands: EDO.3, EDO.16 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Water bridges: A:R.117, A:H.120, D:R.117 Hydrogen bonds: D:R.117 EDO.7: 3 residues within 4Å: Chain B: H.120, G.125 Ligands: EDO.8 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Water bridges: E:R.170, E:R.170 Hydrogen bonds: B:G.125 EDO.8: 5 residues within 4Å: Chain B: R.117, H.120 Chain F: R.117 Ligands: EDO.7, EDO.24 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Water bridges: B:R.117, B:H.120, F:R.117 Hydrogen bonds: F:R.117 EDO.11: 3 residues within 4Å: Chain C: H.120, G.125 Ligands: EDO.12 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:R.170, D:R.170 Hydrogen bonds: C:G.125 EDO.12: 5 residues within 4Å: Chain C: R.117, H.120 Chain E: R.117 Ligands: EDO.11, EDO.20 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:R.117 Water bridges: E:R.117, C:R.117, C:H.120 EDO.15: 3 residues within 4Å: Chain D: H.120, G.125 Ligands: EDO.16 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:R.170, C:R.170 Hydrogen bonds: D:G.125 EDO.16: 5 residues within 4Å: Chain A: R.117 Chain D: R.117, H.120 Ligands: EDO.4, EDO.15 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Water bridges: D:R.117, D:H.120, A:R.117 Hydrogen bonds: A:R.117 EDO.19: 3 residues within 4Å: Chain E: H.120, G.125 Ligands: EDO.20 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Water bridges: B:R.170, B:R.170 Hydrogen bonds: E:G.125 EDO.20: 5 residues within 4Å: Chain C: R.117 Chain E: R.117, H.120 Ligands: EDO.12, EDO.19 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:R.117 Water bridges: C:R.117, E:R.117, E:H.120 EDO.23: 3 residues within 4Å: Chain F: H.120, G.125 Ligands: EDO.24 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Water bridges: A:R.170, A:R.170 Hydrogen bonds: F:G.125 EDO.24: 5 residues within 4Å: Chain B: R.117 Chain F: R.117, H.120 Ligands: EDO.8, EDO.23 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Water bridges: F:R.117, F:H.120, B:R.117 Hydrogen bonds: B:R.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ducati, R.G. et al., Genetic resistance to purine nucleoside phosphorylase inhibition in. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-02-14

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