› 1tmk

X-ray diffraction
2.1Å resolution

YEAST THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (DTMP)

Released:
DOI: 10.2210/pdb1tmk/pdb
PDB entry 1tmk coloured by chain, front view.
PDB entry 1tmk coloured by chain, side view.
PDB entry 1tmk coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation.
Lavie A, Vetter IR, Konrad M, Goody RS, Reinstein J, Schlichting I
Nat Struct Biol 4 601-4 (1997)
PMID: 9253404

Function and Biology Details

Reaction catalysed: 
ATP + dTMP = ADP + dTDP
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132724 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 216 amino acids
Theoretical weight: 24.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P00572 (Residues: 1-216; Coverage: 100%)
Gene names: CDC8, J1715, YJR057W
Sequence domains: Thymidylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand TMP 2 x TMP
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MACSCIENCE
Spacegroup: P21
Unit cell:
a: 36.45Å b: 141.2Å c: 48.75Å
α: 90° β: 109.35° γ: 90°
R-values:
R R work R free
0.18 0.18 0.272
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Synthesis of nucleoside phosphate and phosphonate prodrugs.
Pradere et al. (2014)
6 more

2 mentions without citation

From the similarity analysis of protein cavities to the functional classification of protein families using cavbase.
Kuhn et al. (2006)
1 more