ISDA

Deposition Date 2017-07-28

Release Date 2018-04-18

Last Version Date 2024-01-17

Entry Detail

PDB ID:

5OLN

Keywords:

TRANSFERASE

Title:

X-Ray Structure of the Complex Pyrimidine-nucleoside phosphorylase from Bacillus subtilis at 1.88 A

Biological Source:

Source Organism:

Bacillus subtilis (strain 168) (Taxon ID: 224308)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.88 Å

R-Value Free:

0.23

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Pyrimidine-nucleoside phosphorylase
Gene (Uniprot):pdp
Chain IDs:A, B
Chain Length:434
Number of Molecules:2
Biological Source:Bacillus subtilis (strain 168)

UniProt ID:P39142 Pfam ID:PF02885, PF00591, PF07831 EC:2.4.2.2

Ligand Molecules

EDO

IMD

SO4

Primary Citation

Crystal structure of pyrimidine-nucleoside phosphorylase from Bacillus subtilis in complex with imidazole and sulfate.

Balaev, V.V, Prokofev, I.I, Gabdoulkhakov, A.G, Betzel, C, Lashkov, A.A.Show

Acta Crystallogr F Struct Biol Commun 74 193 197 (2018)

PMID: 29633966 DOI: 10.1107/S2053230X18002935

Abstact

Pyrimidine-nucleoside phosphorylase catalyzes the phosphorolytic cleavage of thymidine and uridine with equal activity. Investigation of this protein is essential for anticancer drug design. Here, the structure of this protein from Bacillus subtilis in complex with imidazole and sulfate is reported at 1.9 Å resolution, which is an improvement on the previously reported structure at 2.6 Å resolution. The localization and position of imidazole in the nucleoside-binding site reflects the possible binding of ligands that possess an imidazole ring.

Legend

Protein

Chemical

Disease

Primary Citation of related structures