SMTL ID : 3h5q.1

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x THM: THYMIDINE(Non-covalent)

THM.1: 8 residues within 4Å: Chain A: T.87, Y.168, R.171, V.177, I.183, S.186, K.190, F.210 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.168, A:V.177, A:I.183, A:F.210 Hydrogen bonds: A:R.171, A:R.171, A:S.186, A:S.186, A:K.190 Water bridges: A:T.87, A:Y.168 THM.4: 8 residues within 4Å: Chain B: T.87, Y.168, R.171, V.177, I.183, S.186, K.190, F.210 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.168, B:V.177, B:I.183, B:F.210 Hydrogen bonds: B:Y.168, B:R.171, B:R.171, B:S.186, B:S.186, B:K.190 Water bridges: B:T.87

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

SO4.2: 5 residues within 4Å: Chain A: R.248, P.268, K.269, D.270, K.386 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.269, A:D.270, A:D.270 Water bridges: A:R.248, A:R.248, A:K.386, A:K.386 Salt bridges: A:R.248 SO4.3: 4 residues within 4Å: Chain A: T.95, K.111, S.113, T.123 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.95, A:S.113, A:T.123 Water bridges: A:T.95, A:T.123 Salt bridges: A:K.111 SO4.5: 5 residues within 4Å: Chain B: R.248, P.268, K.269, D.270, K.386 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.269, B:D.270 Water bridges: B:R.248, B:R.248, B:K.386, B:K.386 Salt bridges: B:R.248 SO4.6: 4 residues within 4Å: Chain B: T.95, K.111, S.113, T.123 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.113, B:T.123 Water bridges: B:T.95, B:T.123 Salt bridges: B:K.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shumilin, I.A. et al., Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus. TO BE PUBLISHED

Release Date

2009-05-26

Peptides

Pyrimidine-nucleoside phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrimidine-nucleoside phosphorylase