SMTL ID : 3fwp.1

X-ray structure of uridine nucleoside phosphorylease from Salmonella typhimurium complexed with phosphate and its inhibitor 2,2'-anhydrouridine at 1.86 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 10 residues within 4Å: Chain B: P.25, G.26, D.27, R.30, R.91, I.92, G.93, T.94 Chain D: R.48 Ligands: ANU.3 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.26, B:D.27, B:T.94, B:T.94 Salt bridges: B:R.30, B:R.91, D:R.48 PO4.5: 9 residues within 4Å: Chain B: R.48 Chain D: P.25, G.26, R.30, R.91, I.92, G.93, T.94 Ligands: ANU.6 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.26, D:T.94, D:E.198 Salt bridges: D:R.30, D:R.91, B:R.48 PO4.8: 8 residues within 4Å: Chain A: R.48 Chain F: P.25, G.26, R.91, I.92, G.93, T.94 Ligands: ANU.9 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:G.26, F:T.94 Water bridges: F:R.30, F:I.92 Salt bridges: F:R.91, A:R.48

3 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain B: E.49, I.69, S.73 Chain D: E.49, I.69, S.73 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:E.49, D:I.69, B:E.49, B:I.69, B:S.73 K.4: 6 residues within 4Å: Chain C: E.49, I.69, S.73 Chain E: E.49, I.69, S.73 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Metal complexes: C:E.49, C:I.69, E:E.49, E:I.69 K.7: 6 residues within 4Å: Chain A: E.49, I.69, S.73 Chain F: E.49, I.69, S.73 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A Metal complexes: F:E.49, F:I.69, F:S.73, A:E.49, A:I.69

3 x ANU: 2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil(Non-covalent)

ANU.3: 15 residues within 4Å: Chain B: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, E.196, M.197, E.198, I.220 Chain D: F.7, H.8, R.48 Ligands: PO4.1 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.220 Hydrogen bonds: B:T.94, B:G.96, B:Q.166, B:R.168, B:R.168, B:E.198, D:H.8, D:R.48 ANU.6: 14 residues within 4Å: Chain B: H.8, R.48 Chain D: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, E.196, M.197, E.198, I.220 Ligands: PO4.5 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:I.220 Hydrogen bonds: D:T.94, D:G.96, D:Q.166, D:R.168, D:R.168, D:E.198, B:H.8, B:R.48 ANU.9: 15 residues within 4Å: Chain A: F.7, H.8, R.48 Chain F: I.69, T.94, T.95, G.96, F.162, Q.166, R.168, Y.195, E.196, M.197, E.198 Ligands: PO4.8 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:G.96, F:Q.166, F:R.168, F:R.168, F:E.198, A:H.8, A:R.48

Links

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Citation

Lashkov, A.A. et al., The X-ray structure of Salmonella typhimurium uridine nucleoside phosphorylase complexed with 2,2'-anhydrouridine, phosphate and potassium ions at 1.86 A resolution. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-01-19

Peptides

Uridine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uridine phosphorylase

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