› 1e2k

X-ray diffraction
1.7Å resolution

Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine

Released:
DOI: 10.2210/pdb1e2k/pdb
PDB entry 1e2k coloured by chain, front view.
PDB entry 1e2k coloured by chain, side view.
PDB entry 1e2k coloured by chain, top view.
Source organism: Human alphaherpesvirus 1 strain 17
Primary publication:
Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine.
Prota A, Vogt J, Pilger B, Perozzo R, Wurth C, Marquez VE, Russ P, Schulz GE, Folkers G, Scapozza L
Biochemistry 39 9597-603 (2000)
PMID: 10924157

Function and Biology Details

Reaction catalysed: 
ATP + thymidine = ADP + thymidine 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145122 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidine kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 331 amino acids
Theoretical weight: 35.78 KDa
Source organism: Human alphaherpesvirus 1 strain 17
Expression system: Escherichia coli
UniProt:
  • Canonical: P0DTH5 (Residues: 46-376; Coverage: 88%)
Gene names: TK, UL23
Sequence domains: Thymidine kinase from herpesvirus
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand TMC 2 x TMC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: C2221
Unit cell:
a: 114Å b: 117.7Å c: 108.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.209 0.252
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The history of N-methanocarbathymidine: the investigation of a conformational concept leads to the discovery of a potent and selective nucleoside antiviral agent.
Marquez et al. (2006)
1 more

2 mentions without citation

Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.
Chen et al. (2009)
1 more