SMTL ID : 3d1v.1

Crystal structure of human PNP complexed with 2-mercapto(3H) quinazolinone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: G.32, S.33, R.84, H.86, N.115, A.116, S.220 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.33, A:A.116, A:S.220 Water bridges: A:Y.88, A:Y.88, A:M.219 Salt bridges: A:R.84, A:H.86 SO4.2: 7 residues within 4Å: Chain A: G.32, S.33, G.34, L.35, G.36, A.65, Q.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.34, A:G.34, A:G.36, A:Q.82 SO4.3: 4 residues within 4Å: Chain A: R.148 Chain B: Y.91, P.92, Q.144 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.148 Hydrogen bonds: B:Q.144 SO4.5: 7 residues within 4Å: Chain B: G.32, S.33, R.84, H.86, N.115, A.116, S.220 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.33, B:A.116, B:S.220 Water bridges: B:Y.88, B:Y.88, B:M.219 Salt bridges: B:R.84, B:H.86 SO4.6: 7 residues within 4Å: Chain B: G.32, S.33, G.34, L.35, G.36, A.65, Q.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.34, B:G.34, B:G.36, B:Q.82 SO4.7: 4 residues within 4Å: Chain B: R.148 Chain C: Y.91, P.92, Q.144 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Salt bridges: B:R.148 Hydrogen bonds: C:Q.144 SO4.9: 7 residues within 4Å: Chain C: G.32, S.33, R.84, H.86, N.115, A.116, S.220 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.33, C:A.116, C:S.220 Water bridges: C:Y.88, C:Y.88, C:M.219 Salt bridges: C:R.84, C:H.86 SO4.10: 7 residues within 4Å: Chain C: G.32, S.33, G.34, L.35, G.36, A.65, Q.82 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.34, C:G.34, C:G.36, C:Q.82 SO4.11: 4 residues within 4Å: Chain A: Y.91, P.92, Q.144 Chain C: R.148 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.148 Hydrogen bonds: A:Q.144

3 x D1V: 2-mercapto(3H)quinazolinone(Non-covalent)

D1V.4: 9 residues within 4Å: Chain A: A.116, A.117, G.118, F.200, E.201, V.217, M.219, T.242, N.243 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.116, A:F.200 Hydrogen bonds: A:E.201 D1V.8: 9 residues within 4Å: Chain B: A.116, A.117, G.118, F.200, E.201, V.217, M.219, T.242, N.243 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.116, B:F.200 Hydrogen bonds: B:E.201 D1V.12: 9 residues within 4Å: Chain C: A.116, A.117, G.118, F.200, E.201, V.217, M.219, T.242, N.243 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.116, C:F.200 Hydrogen bonds: C:E.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timmers, L.F. et al., Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function. Arch.Biochem.Biophys. (2008)

Release Date

2009-07-14

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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