SMTL ID : 5ko5.1

Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with cytosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-trimer

Ligands

3 x CYT: 6-AMINOPYRIMIDIN-2(1H)-ONE(Non-covalent)

CYT.1: 12 residues within 4Å: Chain A: L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, N.245, S.247, I.257, V.262 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.262 Hydrogen bonds: A:L.118, A:G.120, A:N.245, A:N.245, A:S.247 Water bridges: A:Y.202, A:E.203, A:E.203, A:M.221 pi-Stacking: A:Y.202 CYT.5: 12 residues within 4Å: Chain B: L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, N.245, S.247, I.257, V.262 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.262 Hydrogen bonds: B:G.120, B:N.245, B:N.245, B:S.247 Water bridges: B:E.203, B:E.203, B:M.221 pi-Stacking: B:Y.202 CYT.9: 12 residues within 4Å: Chain C: L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, N.245, S.247, I.257, V.262 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.262 Hydrogen bonds: C:G.120, C:N.245, C:N.245, C:S.247 Water bridges: C:Y.202, C:E.203, C:E.203, C:M.221 pi-Stacking: C:Y.202

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

EDO.2: 8 residues within 4Å: Chain A: G.34, S.35, R.86, H.88, N.117, L.118, M.221, S.222 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.35, A:R.86, A:L.118, A:M.221 Water bridges: A:L.118, A:L.118, A:S.222 EDO.3: 4 residues within 4Å: Chain A: D.155, E.156, F.157, G.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.155 Water bridges: A:K.106 EDO.4: 4 residues within 4Å: Chain A: K.106, L.107, E.156, F.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.106, A:F.157 EDO.6: 8 residues within 4Å: Chain B: G.34, S.35, R.86, H.88, N.117, L.118, M.221, S.222 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.35, B:R.86, B:L.118, B:M.221 Water bridges: B:L.118, B:L.118, B:S.222 EDO.7: 4 residues within 4Å: Chain B: D.155, E.156, F.157, G.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.155 Water bridges: B:K.106 EDO.8: 4 residues within 4Å: Chain B: K.106, L.107, E.156, F.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.106, B:F.157 EDO.10: 8 residues within 4Å: Chain C: G.34, S.35, R.86, H.88, N.117, L.118, M.221, S.222 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.35, C:R.86, C:L.118, C:M.221 Water bridges: C:L.118, C:L.118, C:S.222 EDO.11: 4 residues within 4Å: Chain C: D.155, E.156, F.157, G.158 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.155 Water bridges: C:K.106 EDO.12: 4 residues within 4Å: Chain C: K.106, L.107, E.156, F.157 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.106, C:F.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torini, J.R. et al., The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs. PLoS ONE (2018)

Release Date

2017-08-09

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Purine nucleoside phosphorylase

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