SMTL ID : 6bj6.1

Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 2-{[(S)-benzenesulfinyl]methyl}benzoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-trimer

Ligands

12 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: 6 residues within 4Å: Chain A: Y.9, K.106, L.107, E.156, F.157, C.233 No protein-ligand interaction detected (PLIP) DMS.4: 7 residues within 4Å: Chain A: V.63, A.64, E.91, G.92, Y.93, E.97 Chain B: P.152 No protein-ligand interaction detected (PLIP) DMS.6: 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.7: 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.8: 6 residues within 4Å: Chain B: Y.9, K.106, L.107, E.156, F.157, C.233 No protein-ligand interaction detected (PLIP) DMS.9: 7 residues within 4Å: Chain B: V.63, A.64, E.91, G.92, Y.93, E.97 Chain C: P.152 No protein-ligand interaction detected (PLIP) DMS.11: 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.12: 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.13: 6 residues within 4Å: Chain C: Y.9, K.106, L.107, E.156, F.157, C.233 No protein-ligand interaction detected (PLIP) DMS.14: 7 residues within 4Å: Chain A: P.152 Chain C: V.63, A.64, E.91, G.92, Y.93, E.97 No protein-ligand interaction detected (PLIP)

3 x DTS: 2-{[(S)-phenylsulfinyl]methyl}benzoic acid(Non-covalent)

DTS.5: 19 residues within 4Å: Chain A: S.35, H.88, Y.90, N.117, L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, S.222, A.244, N.245, H.259, V.262, L.263 Chain B: F.161 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.118, A:Y.202, A:Y.202, A:Y.202, A:V.262, A:L.263 Hydrogen bonds: A:S.35, A:S.35, A:N.117, A:M.221 Water bridges: A:S.35, A:S.222 Salt bridges: A:H.88 pi-Stacking: B:F.161 DTS.10: 19 residues within 4Å: Chain B: S.35, H.88, Y.90, N.117, L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, S.222, A.244, N.245, H.259, V.262, L.263 Chain C: F.161 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.118, B:Y.202, B:Y.202, B:Y.202, B:V.262, B:L.263 Hydrogen bonds: B:S.35, B:S.35, B:N.117, B:M.221 Water bridges: B:S.35, B:S.222 Salt bridges: B:H.88 pi-Stacking: C:F.161 DTS.15: 19 residues within 4Å: Chain A: F.161 Chain C: S.35, H.88, Y.90, N.117, L.118, A.119, G.120, Y.202, E.203, V.219, G.220, M.221, S.222, A.244, N.245, H.259, V.262, L.263 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.118, C:Y.202, C:Y.202, C:Y.202, C:V.262, C:L.263 Hydrogen bonds: C:S.35, C:S.35, C:N.117, C:M.221 Water bridges: C:S.35, C:S.222 Salt bridges: C:H.88 pi-Stacking: A:F.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faheem, M. et al., Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 2-{[(S)-benzenesulfinyl]methyl}benzoic acid. 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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