SMTL ID : 1v45.1

Crystal Structure of human PNP complexed with 3-deoxyguanosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.86 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: P.91, Q.143 Chain C: R.147 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.143, A:Q.143 Salt bridges: C:R.147 SO4.2: 5 residues within 4Å: Chain A: S.32, G.33, L.34, G.35, Q.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.33, A:G.33, A:G.35, A:Q.81 SO4.3: 8 residues within 4Å: Chain A: G.31, S.32, R.83, H.85, N.114, A.115, S.219 Ligands: 3DG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.32, A:A.115, A:S.219 Water bridges: A:M.218 Salt bridges: A:R.83, A:H.85 SO4.5: 3 residues within 4Å: Chain A: R.147 Chain B: P.91, Q.143 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.143, B:Q.143 Salt bridges: A:R.147 SO4.6: 5 residues within 4Å: Chain B: S.32, G.33, L.34, G.35, Q.81 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.33, B:G.33, B:G.35, B:Q.81 SO4.7: 8 residues within 4Å: Chain B: G.31, S.32, R.83, H.85, N.114, A.115, S.219 Ligands: 3DG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.32, B:A.115, B:S.219 Water bridges: B:M.218 Salt bridges: B:R.83, B:H.85 SO4.9: 3 residues within 4Å: Chain B: R.147 Chain C: P.91, Q.143 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Salt bridges: B:R.147 Hydrogen bonds: C:Q.143, C:Q.143 SO4.10: 5 residues within 4Å: Chain C: S.32, G.33, L.34, G.35, Q.81 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.33, C:G.33, C:G.35, C:Q.81 SO4.11: 8 residues within 4Å: Chain C: G.31, S.32, R.83, H.85, N.114, A.115, S.219 Ligands: 3DG.12 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.32, C:A.115, C:S.219 Water bridges: C:M.218 Salt bridges: C:R.83, C:H.85

3 x 3DG: 9-(3-DEOXY-BETA-D-RIBOFURANOSYL)GUANINE(Non-covalent)

3DG.4: 15 residues within 4Å: Chain A: Y.87, A.115, A.116, G.117, F.199, E.200, V.216, G.217, M.218, T.241, N.242, V.244, H.256 Chain C: F.158 Ligands: SO4.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.115, A:M.218, A:T.241, A:N.242 Water bridges: A:S.198, A:E.200 Salt bridges: A:E.200 pi-Stacking: A:F.199 Hydrophobic interactions: C:F.158 3DG.8: 15 residues within 4Å: Chain A: F.158 Chain B: Y.87, A.115, A.116, G.117, F.199, E.200, V.216, G.217, M.218, T.241, N.242, V.244, H.256 Ligands: SO4.7 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.115, B:M.218, B:T.241, B:N.242 Water bridges: B:S.198, B:E.200 Salt bridges: B:E.200 pi-Stacking: B:F.199 Hydrophobic interactions: A:F.158 3DG.12: 15 residues within 4Å: Chain B: F.158 Chain C: Y.87, A.115, A.116, G.117, F.199, E.200, V.216, G.217, M.218, T.241, N.242, V.244, H.256 Ligands: SO4.11 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:A.115, C:M.218, C:T.241, C:N.242 Water bridges: C:S.198, C:E.200 Salt bridges: C:E.200 pi-Stacking: C:F.199 Hydrophobic interactions: B:F.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Canduri, F. et al., Structure of human PNP complexed with ligands. Acta Crystallogr.,Sect.D (2005)

Release Date

2004-12-14

Peptides

Purine nucleoside phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

C
E

Purine nucleoside phosphorylase

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