SMTL ID : 3bgs.1

Structure of human purine nucleoside phosphorylase with L-DADMe-ImmH and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: E.153, D.157, R.158 Chain B: H.257 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.157, A:D.157, A:R.158 Water bridges: A:F.159 Salt bridges: B:H.257 PO4.2: 8 residues within 4Å: Chain A: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: DIH.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.33, A:T.114, A:A.116, A:S.220 Water bridges: A:G.32, A:S.33, A:M.219, A:M.219 Salt bridges: A:R.84, A:H.86 PO4.3: 3 residues within 4Å: Chain A: R.148 Chain B: P.92, Q.144 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.144, B:Q.144 Water bridges: A:M.1 Salt bridges: A:R.148 PO4.5: 4 residues within 4Å: Chain B: E.153, D.157, R.158 Chain C: H.257 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.157, B:D.157, B:R.158 Water bridges: B:F.159 Salt bridges: C:H.257 PO4.6: 8 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: DIH.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.33, B:T.114, B:A.116, B:S.220 Water bridges: B:G.32, B:S.33, B:M.219, B:M.219 Salt bridges: B:R.84, B:H.86 PO4.7: 3 residues within 4Å: Chain B: R.148 Chain C: P.92, Q.144 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Water bridges: B:M.1 Salt bridges: B:R.148 Hydrogen bonds: C:Q.144, C:Q.144 PO4.9: 4 residues within 4Å: Chain A: H.257 Chain C: E.153, D.157, R.158 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.157, C:D.157, C:R.158 Water bridges: C:F.159 Salt bridges: A:H.257 PO4.10: 8 residues within 4Å: Chain C: G.32, S.33, R.84, H.86, N.115, A.116, S.220 Ligands: DIH.12 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.33, C:T.114, C:A.116, C:S.220 Water bridges: C:G.32, C:S.33, C:M.219, C:M.219 Salt bridges: C:R.84, C:H.86 PO4.11: 3 residues within 4Å: Chain A: P.92, Q.144 Chain C: R.148 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:M.1 Salt bridges: C:R.148 Hydrogen bonds: A:Q.144, A:Q.144

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: 17 residues within 4Å: Chain A: H.86, 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: PO4.2 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.88, A:Y.88, A:E.201, A:N.243, A:N.243, A:H.257 Water bridges: A:E.201, A:M.219 pi-Stacking: A:F.200 Hydrophobic interactions: C:F.159 DIH.8: 17 residues within 4Å: Chain A: F.159 Chain B: H.86, 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: PO4.6 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.88, B:Y.88, B:E.201, B:N.243, B:N.243, B:H.257 Water bridges: B:E.201, B:M.219 pi-Stacking: B:F.200 Hydrophobic interactions: A:F.159 DIH.12: 17 residues within 4Å: Chain B: F.159 Chain C: H.86, 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: PO4.10 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:F.159 Hydrogen bonds: C:Y.88, C:Y.88, C:E.201, C:N.243, C:N.243, C:H.257 Water bridges: C:E.201, C:M.219 pi-Stacking: C:F.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rinaldo-Matthis, A. et al., L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase. J.Am.Chem.Soc. (2008)

Release Date

2008-01-08

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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