SMTL ID : 6bj7.1

Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 4-chloro-6-methylpyrimidin-2-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-trimer

Ligands

15 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 12 residues within 4Å: Chain A: A.7, N.95, Q.96, A.99, R.103, V.148, L.149, V.150, G.151, P.152, Q.154, I.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.103, A:R.103 Water bridges: A:Q.154, A:Q.154 DMS.2: 6 residues within 4Å: Chain A: P.159, P.162, D.163, C.231, H.232, G.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.163 DMS.3: 8 residues within 4Å: Chain A: D.28, I.29, R.78, R.111, V.112, L.284, P.285, L.286 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.28 DMS.4: 9 residues within 4Å: Chain A: S.35, L.118, Y.202, M.221, H.259, V.262 Chain B: F.161 Ligands: DMS.5, DU7.6 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A pi-Cation interactions: B:F.161 Hydrogen bonds: A:Y.202, A:H.259 DMS.5: 9 residues within 4Å: Chain A: G.34, S.35, R.86, H.88, N.117, L.118, S.222, T.223 Ligands: DMS.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.35, A:L.118 DMS.7: 12 residues within 4Å: Chain B: A.7, N.95, Q.96, A.99, R.103, V.148, L.149, V.150, G.151, P.152, Q.154, I.229 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.103, B:R.103 Water bridges: B:Q.154, B:Q.154 DMS.8: 6 residues within 4Å: Chain B: P.159, P.162, D.163, C.231, H.232, G.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.163 DMS.9: 8 residues within 4Å: Chain B: D.28, I.29, R.78, R.111, V.112, L.284, P.285, L.286 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.28 DMS.10: 9 residues within 4Å: Chain B: S.35, L.118, Y.202, M.221, H.259, V.262 Chain C: F.161 Ligands: DMS.11, DU7.12 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.202, B:H.259 pi-Cation interactions: C:F.161 DMS.11: 9 residues within 4Å: Chain B: G.34, S.35, R.86, H.88, N.117, L.118, S.222, T.223 Ligands: DMS.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.35, B:L.118 DMS.13: 12 residues within 4Å: Chain C: A.7, N.95, Q.96, A.99, R.103, V.148, L.149, V.150, G.151, P.152, Q.154, I.229 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.103, C:R.103 Water bridges: C:Q.154, C:Q.154 DMS.14: 6 residues within 4Å: Chain C: P.159, P.162, D.163, C.231, H.232, G.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.163 DMS.15: 8 residues within 4Å: Chain C: D.28, I.29, R.78, R.111, V.112, L.284, P.285, L.286 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:D.28 DMS.16: 9 residues within 4Å: Chain A: F.161 Chain C: S.35, L.118, Y.202, M.221, H.259, V.262 Ligands: DMS.17, DU7.18 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.202, C:H.259 pi-Cation interactions: A:F.161 DMS.17: 9 residues within 4Å: Chain C: G.34, S.35, R.86, H.88, N.117, L.118, S.222, T.223 Ligands: DMS.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.35, C:L.118

3 x DU7: 4-chloro-6-methylpyrimidin-2-amine(Non-covalent)

DU7.6: 14 residues within 4Å: Chain A: L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, A.244, N.245, S.247, I.257, V.262 Ligands: DMS.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.118, A:A.244, A:V.262 Hydrogen bonds: A:G.120, A:N.245, A:S.247, A:S.247 Water bridges: A:E.203 Salt bridges: A:E.203 pi-Stacking: A:Y.202 DU7.12: 14 residues within 4Å: Chain B: L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, A.244, N.245, S.247, I.257, V.262 Ligands: DMS.10 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.118, B:A.244, B:V.262 Hydrogen bonds: B:G.120, B:N.245, B:S.247, B:S.247 Water bridges: B:E.203 Salt bridges: B:E.203 pi-Stacking: B:Y.202 DU7.18: 14 residues within 4Å: Chain C: L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, A.244, N.245, S.247, I.257, V.262 Ligands: DMS.16 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.118, C:A.244, C:V.262 Hydrogen bonds: C:G.120, C:N.245, C:S.247, C:S.247 Water bridges: C:E.203 Salt bridges: C:E.203 pi-Stacking: C:Y.202

Links

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Citation

Faheem, M. et al., Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 4-chloro-6-methylpyrimidin-2-amine. To Be Published

Release Date

2018-11-07

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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