› 2b8t

X-ray diffraction
2Å resolution

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

Released:
DOI: 10.2210/pdb2b8t/pdb
PDB entry 2b8t coloured by chain, front view.
PDB entry 2b8t coloured by chain, side view.
PDB entry 2b8t coloured by chain, top view.
Source organism: Ureaplasma parvum
Primary publication:
Structure of the substrate complex of thymidine kinase from Ureaplasma urealyticum and investigations of possible drug targets for the enzyme.
Kosinska U, Carnrot C, Eriksson S, Wang L, Eklund H
FEBS J 272 6365-72 (2005)
PMID: 16336273

Function and Biology Details

Reaction catalysed: 
ATP + thymidine = ADP + thymidine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192938 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidine kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 223 amino acids
Theoretical weight: 25.44 KDa
Source organism: Ureaplasma parvum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9PPP5 (Residues: 1-223; Coverage: 100%)
Gene names: UU594, tdk
Sequence domains: Thymidine kinase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand THM 4 x THM
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P21
Unit cell:
a: 57.158Å b: 115.649Å c: 64.474Å
α: 90° β: 101.02° γ: 90°
R-values:
R R work R free
0.197 0.195 0.235
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Carboranyl thymidine analogues for neutron capture therapy.
Tjarks et al. (2007)
1 more

9 mentions without citation

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
Mysinger et al. (2012)
8 more