› 2tmk

X-ray diffraction
2.4Å resolution

YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE MONOPHOSPHATE (AZT-MP)

Released:
DOI: 10.2210/pdb2tmk/pdb
PDB entry 2tmk coloured by chain, front view.
PDB entry 2tmk coloured by chain, side view.
PDB entry 2tmk 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 SO4 2 x SO4
Ligand ATM 2 x ATM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS
Spacegroup: P21
Unit cell:
a: 37.42Å b: 144.2Å c: 49.72Å
α: 90° β: 110.9° γ: 90°
R-values:
R R work R free
0.182 0.182 0.253
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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

2 mentions without citation

Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.
De et al. (2005)
1 more