› 1nmy

X-ray diffraction
1.6Å resolution

Crystal structure of human thymidylate kinase with FLTMP and AppNHp

Released:
DOI: 10.2210/pdb1nmy/pdb
PDB entry 1nmy coloured by chain, front view.
PDB entry 1nmy coloured by chain, side view.
PDB entry 1nmy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of human thymidylate kinase in complex with prodrugs: implications for the structure-based design of novel compounds.
Ostermann N, Segura-Peña D, Meier C, Veit T, Monnerjahn C, Konrad M, Lavie A
Biochemistry 42 2568-77 (2003)
PMID: 12614151

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-150116 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chain: A
Molecule details ›
Chain: A
Length: 209 amino acids
Theoretical weight: 23.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23919 (Residues: 4-212; Coverage: 99%)
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 MG 2 x MG
Ligand FDM 1 x FDM
Ligand ADP 1 x ADP
Ligand ANP 1 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P43212
Unit cell:
a: 101.258Å b: 101.258Å c: 49.781Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.175 0.22
Expression system: Escherichia coli

Quick links

Citations

20 citation in other articles

Metabolism of 3'-deoxy-3'-[F-18]fluorothymidine in proliferating A549 cells: validations for positron emission tomography.
Grierson et al. (2004)
19 more

3 mentions without citation

Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria.
Nocek et al. (2008)
2 more