SMTL ID : 3mb8.1

Crystal structure of purine nucleoside phosphorylase from toxoplasma gondii in complex with immucillin-H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

6 x IMH: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL(Non-covalent)

IMH.1: 16 residues within 4Å: Chain A: I.71, R.93, T.96, C.97, G.98, F.165, I.185, D.186, M.187, E.188, D.210, P.213, W.216 Chain B: H.12 Ligands: PO4.2, GOL.8 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:H.12, B:R.50, A:T.96, A:T.96, A:M.187, A:E.188, A:E.188 Water bridges: A:F.165, A:Q.167 IMH.5: 16 residues within 4Å: Chain A: H.12 Chain B: I.71, R.93, T.96, C.97, G.98, F.165, I.185, D.186, M.187, E.188, D.210, P.213, W.216 Ligands: GOL.4, PO4.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.186, B:M.187, B:E.188, B:E.188, A:H.12 Water bridges: B:F.165, B:Q.167 IMH.9: 16 residues within 4Å: Chain C: I.71, R.93, T.96, C.97, G.98, F.165, I.185, D.186, M.187, E.188, D.210, P.213, W.216 Chain D: H.12 Ligands: PO4.10, GOL.16 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:H.12, D:R.50, C:T.96, C:T.96, C:M.187, C:E.188, C:E.188 Water bridges: C:F.165, C:Q.167 IMH.13: 16 residues within 4Å: Chain C: H.12 Chain D: I.71, R.93, T.96, C.97, G.98, F.165, I.185, D.186, M.187, E.188, D.210, P.213, W.216 Ligands: GOL.12, PO4.14 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.186, D:M.187, D:E.188, D:E.188, C:H.12 Water bridges: D:F.165, D:Q.167 IMH.17: 16 residues within 4Å: Chain E: I.71, R.93, T.96, C.97, G.98, F.165, I.185, D.186, M.187, E.188, D.210, P.213, W.216 Chain F: H.12 Ligands: PO4.18, GOL.24 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:T.96, E:T.96, E:M.187, E:E.188, E:E.188, F:H.12, F:R.50 Water bridges: E:F.165, E:Q.167 IMH.21: 16 residues within 4Å: Chain E: H.12 Chain F: I.71, R.93, T.96, C.97, G.98, F.165, I.185, D.186, M.187, E.188, D.210, P.213, W.216 Ligands: GOL.20, PO4.22 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:D.186, F:M.187, F:E.188, F:E.188, E:H.12 Water bridges: F:F.165, F:Q.167

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

PO4.2: 8 residues within 4Å: Chain A: V.27, G.28, R.32, R.93, G.95, T.96 Chain B: R.50 Ligands: IMH.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.28, A:T.96, A:T.96, A:E.188 Salt bridges: A:R.32, A:R.93, B:R.50 PO4.6: 8 residues within 4Å: Chain A: R.50 Chain B: V.27, G.28, R.32, R.93, G.95, T.96 Ligands: IMH.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.28, B:T.96, B:T.96 Salt bridges: B:R.32, B:R.93, A:R.50 PO4.10: 8 residues within 4Å: Chain C: V.27, G.28, R.32, R.93, G.95, T.96 Chain D: R.50 Ligands: IMH.9 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.28, C:T.96, C:T.96, C:E.188 Salt bridges: C:R.32, C:R.93, D:R.50 PO4.14: 8 residues within 4Å: Chain C: R.50 Chain D: V.27, G.28, R.32, R.93, G.95, T.96 Ligands: IMH.13 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.28, D:T.96, D:T.96 Salt bridges: D:R.32, D:R.93, C:R.50 PO4.18: 8 residues within 4Å: Chain E: V.27, G.28, R.32, R.93, G.95, T.96 Chain F: R.50 Ligands: IMH.17 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.28, E:T.96, E:T.96, E:E.188 Salt bridges: E:R.32, E:R.93, F:R.50 PO4.22: 8 residues within 4Å: Chain E: R.50 Chain F: V.27, G.28, R.32, R.93, G.95, T.96 Ligands: IMH.21 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.28, F:T.96, F:T.96 Salt bridges: F:R.32, F:R.93, E:R.50

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.14, R.16, D.19, L.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.14, A:R.16, A:D.19, A:L.46 GOL.4: 8 residues within 4Å: Chain A: P.11, H.12, R.14, N.49, R.50 Chain B: Y.221, A.223 Ligands: IMH.5 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.221, A:P.11, A:N.49, A:R.50 Water bridges: B:T.96, A:R.14, A:N.49 GOL.7: 4 residues within 4Å: Chain B: R.14, R.16, D.19, L.46 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.14, B:R.16 Water bridges: B:E.45 GOL.8: 8 residues within 4Å: Chain A: Y.221, A.223 Chain B: P.11, H.12, R.14, N.49, R.50 Ligands: IMH.1 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.14, B:N.49, B:R.50, A:Y.221 Water bridges: B:N.49, A:D.29, A:T.96 GOL.11: 4 residues within 4Å: Chain C: R.14, R.16, D.19, L.46 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.14, C:R.16, C:D.19, C:L.46 GOL.12: 8 residues within 4Å: Chain C: P.11, H.12, R.14, N.49, R.50 Chain D: Y.221, A.223 Ligands: IMH.13 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:P.11, C:N.49, C:R.50, D:Y.221 Water bridges: C:R.14, C:N.49, D:T.96 GOL.15: 4 residues within 4Å: Chain D: R.14, R.16, D.19, L.46 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.14, D:R.16 Water bridges: D:E.45 GOL.16: 8 residues within 4Å: Chain C: Y.221, A.223 Chain D: P.11, H.12, R.14, N.49, R.50 Ligands: IMH.9 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Y.221, D:R.14, D:N.49, D:R.50 Water bridges: C:D.29, C:T.96, D:N.49 GOL.19: 4 residues within 4Å: Chain E: R.14, R.16, D.19, L.46 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.14, E:R.16, E:D.19, E:L.46 GOL.20: 8 residues within 4Å: Chain E: P.11, H.12, R.14, N.49, R.50 Chain F: Y.221, A.223 Ligands: IMH.21 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:P.11, E:N.49, E:R.50, F:Y.221 Water bridges: E:R.14, E:N.49, F:T.96 GOL.23: 4 residues within 4Å: Chain F: R.14, R.16, D.19, L.46 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.14, F:R.16 Water bridges: F:E.45 GOL.24: 8 residues within 4Å: Chain E: Y.221, A.223 Chain F: P.11, H.12, R.14, N.49, R.50 Ligands: IMH.17 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.14, F:N.49, F:R.50, E:Y.221 Water bridges: F:N.49, E:D.29, E:T.96

Links

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Citation

Donaldson, T.M. et al., Inhibition and Structure of Toxoplasma gondii Purine Nucleoside Phosphorylase. Eukaryot Cell (2014)

Release Date

2011-04-06

Peptides

Purine nucleoside phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Purine nucleoside phosphorylase