SMTL ID : 1rsz.1

Structure of human purine nucleoside phosphorylase in complex with DADMe-Immucillin-H and sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: DIH.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.33, A:A.116, A:S.220, A:S.220 Water bridges: A:M.219, A:M.219 Salt bridges: A:R.84, A:H.86 SO4.2: 3 residues within 4Å: Chain A: R.148 Chain C: P.92, Q.144 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.144 Water bridges: C:L.93 Salt bridges: A:R.148 SO4.3: 4 residues within 4Å: Chain A: N.3, R.148, G.149 Chain C: G.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.3, A:R.148 Water bridges: A:R.148 Salt bridges: A:R.148 SO4.5: 8 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: DIH.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.33, B:A.116, B:S.220, B:S.220 Water bridges: B:M.219, B:M.219 Salt bridges: B:R.84, B:H.86 SO4.6: 3 residues within 4Å: Chain A: P.92, Q.144 Chain B: R.148 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.144 Water bridges: A:L.93 Salt bridges: B:R.148 SO4.7: 4 residues within 4Å: Chain A: G.90 Chain B: N.3, R.148, G.149 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.3, B:R.148 Water bridges: B:R.148 Salt bridges: B:R.148 SO4.9: 8 residues within 4Å: Chain C: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: DIH.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.33, C:A.116, C:S.220, C:S.220 Water bridges: C:M.219, C:M.219 Salt bridges: C:R.84, C:H.86 SO4.10: 3 residues within 4Å: Chain B: P.92, Q.144 Chain C: R.148 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.148 Hydrogen bonds: B:Q.144 Water bridges: B:L.93 SO4.11: 4 residues within 4Å: Chain B: G.90 Chain C: N.3, R.148, G.149 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.3, C:R.148 Water bridges: C:R.148 Salt bridges: C:R.148

3 x DIH: 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

DIH.4: 16 residues within 4Å: Chain A: Y.88, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, T.242, N.243, V.245, H.257, V.260 Chain B: F.159 Ligands: SO4.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.88, A:E.201, A:N.243, A:N.243, A:H.257 Water bridges: A:E.201, A:E.201, A:M.219 pi-Stacking: A:F.200 DIH.8: 16 residues within 4Å: Chain B: Y.88, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, T.242, N.243, V.245, H.257, V.260 Chain C: F.159 Ligands: SO4.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.88, B:E.201, B:N.243, B:N.243, B:H.257 Water bridges: B:E.201, B:E.201, B:M.219 pi-Stacking: B:F.200 DIH.12: 16 residues within 4Å: Chain A: F.159 Chain C: Y.88, A.116, A.117, G.118, F.200, E.201, V.217, G.218, M.219, T.242, N.243, V.245, H.257, V.260 Ligands: SO4.9 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.88, C:E.201, C:N.243, C:N.243, C:H.257 Water bridges: C:E.201, C:E.201, C:M.219 pi-Stacking: C:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, W. et al., Structural comparison of human and malarial purine nucleoside phosphorylases. To be Published

Release Date

2005-02-22

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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