› 1e2e

X-ray diffraction
2Å resolution

Human thymidylate kinase complexed with thymidine monophosphate, adenosine diphosphate,a magnesium-ion and ALf3

Released:
DOI: 10.2210/pdb1e2e/pdb
PDB entry 1e2e coloured by chain, front view.
PDB entry 1e2e coloured by chain, side view.
PDB entry 1e2e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate.
Ostermann N, Schlichting I, Brundiers R, Konrad M, Reinstein J, Veit T, Goody RS, Lavie A
Structure 8 629-42 (2000)
PMID: 10873853

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-150117 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chain: A
Molecule details ›
Chain: A
Length: 215 amino acids
Theoretical weight: 24.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23919 (Residues: 1-212; Coverage: 100%)
Gene names: CDC8, DTYMK, TMPK, TYMK
Sequence domains: Thymidylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

4 bound ligands:
Ligand TMP 1 x TMP
Ligand ADP 1 x ADP
Ligand MG 2 x MG
Ligand AF3 1 x AF3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P43212
Unit cell:
a: 101.6Å b: 101.6Å c: 49.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.272
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Nucleoside analogs and tuberculosis: new weapons against an old enemy.
Ferrari et al. (2015)
2 more

1 mention without citation

Ligand and interfacial dynamics in a homodimeric hemoglobin.
Gupta et al. (2016)