› 2xx3

X-ray diffraction
2Å resolution

HUMAN THYMIDYLATE KINASE COMPLEXED WITH thymidine butenyl phosphonate monophosphate and ADP

Released:
DOI: 10.2210/pdb2xx3/pdb
PDB entry 2xx3 coloured by chain, front view.
PDB entry 2xx3 coloured by chain, side view.
PDB entry 2xx3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Novel antiviral C5-substituted pyrimidine acyclic nucleoside phosphonates selected as human thymidylate kinase substrates.
Topalis D, Pradère U, Roy V, Caillat C, Azzouzi A, Broggi J, Snoeck R, Andrei G, Lin J, Eriksson S, Alexandre JA, El-Amri C, Deville-Bonne D, Meyer P, Balzarini J, Agrofoglio LA
J Med Chem 54 222-32 (2011)
PMID: 21128666

Function and Biology Details

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

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: 232 amino acids
Theoretical weight: 26.03 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 ADP 1 x ADP
Ligand MG 1 x MG
Ligand TAE 1 x TAE
Ligand NO3 1 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2
Unit cell:
a: 102.44Å b: 38.32Å c: 73.16Å
α: 90° β: 123.07° γ: 90°
R-values:
R R work R free
0.191 0.188 0.235
Expression system: Escherichia coli

Quick links

Citations

6 review citations

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