SMTL ID : 3f8w.1

Crystal structure of Schistosoma mansoni purine nucleoside phosphorylase in complex with adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x ADN: ADENOSINE(Non-covalent)

ADN.1: 16 residues within 4Å: Chain A: S.35, Y.90, A.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, T.244, N.245, H.259, V.262 Chain B: F.161 Ligands: SO4.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.35, A:Y.90, A:Y.202, A:M.221, A:T.244, A:N.245, A:N.245, A:H.259 Water bridges: A:Y.194 pi-Stacking: A:Y.202 ADN.5: 17 residues within 4Å: Chain B: S.35, H.88, Y.90, A.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, T.244, N.245, H.259, V.262 Chain C: F.161 Ligands: SO4.6 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:S.35, B:Y.90, B:Y.90, B:Y.202, B:Y.202, B:M.221, B:N.245, B:N.245 Water bridges: B:A.118, B:E.203, B:E.203 pi-Stacking: B:Y.202 ADN.7: 17 residues within 4Å: Chain A: F.161 Chain C: S.35, H.88, Y.90, A.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, T.244, N.245, H.259, V.262 Ligands: SO4.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.35, C:Y.90, C:Y.202, C:M.221, C:T.244, C:N.245, C:N.245 Water bridges: C:E.203, C:E.203 pi-Stacking: C:Y.202

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: G.34, S.35, R.86, H.88, N.117, A.118, S.222 Ligands: ADN.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.35, A:S.35, A:A.118, A:S.222, A:S.222 Salt bridges: A:R.86, A:H.88 SO4.6: 9 residues within 4Å: Chain B: G.34, S.35, H.66, R.86, H.88, N.117, A.118, S.222 Ligands: ADN.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.35, B:S.35, B:A.118, B:S.222, B:S.222 Water bridges: B:M.221 Salt bridges: B:H.66, B:R.86, B:H.88 SO4.8: 8 residues within 4Å: Chain C: G.34, S.35, R.86, H.88, N.117, A.118, S.222 Ligands: ADN.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.35, C:S.35, C:A.118, C:S.222, C:S.222 Water bridges: C:M.221 Salt bridges: C:R.86, C:H.88

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

DMS.3: 8 residues within 4Å: Chain A: N.95, D.96, A.99, R.103, I.148, L.149, V.150, Q.154 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.103, A:R.103 Water bridges: A:Q.154, A:Q.154 Salt bridges: A:D.96 DMS.4: 8 residues within 4Å: Chain B: N.95, D.96, A.99, R.103, I.148, L.149, V.150, Q.154 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.103, B:R.103 Water bridges: B:Q.154, B:Q.154 Salt bridges: B:D.96 DMS.9: 7 residues within 4Å: Chain C: N.95, D.96, A.99, R.103, I.148, V.150, Q.154 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.103, C:R.103 Water bridges: C:Q.154, C:Q.154 Salt bridges: C:D.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pereira, H.M. et al., Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni. Acta Crystallogr.,Sect.D (2010)

Release Date

2009-11-24

Peptides

Purine-nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Purine-nucleoside phosphorylase

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