› 3hjn

X-ray diffraction
2.1Å resolution

Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima

Released:
DOI: 10.2210/pdb3hjn/pdb
PDB entry 3hjn coloured by chain, front view.
PDB entry 3hjn coloured by chain, side view.
PDB entry 3hjn coloured by chain, top view.
Source organism: Thermotoga maritima MSB8
Entry authors: Yoshikawa S, Nakagawa N, Shirouzu M, Yokoyama S, Kuramitsu S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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-194719 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 197 amino acids
Theoretical weight: 22.89 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9X0I3 (Residues: 1-197; Coverage: 100%)
Gene names: TM_1099, tmk
Sequence domains: Thymidylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

3 bound ligands:
Ligand ADP 2 x ADP
Ligand TYD 2 x TYD
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: I222
Unit cell:
a: 51.587Å b: 127.05Å c: 133.519Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.285
Expression system: Escherichia coli

Quick links