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X-ray diffraction
1.6Å resolution

Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

Released:
DOI: 10.2210/pdb2plr/pdb
PDB entry 2plr coloured by chain, front view.
PDB entry 2plr coloured by chain, side view.
PDB entry 2plr coloured by chain, top view.
Source organism: Sulfurisphaera tokodaii str. 7
Entry authors: Kanaujia SP, Jeyakanthan J, Rafi ZA, Sekar K, Nakagawa N, Ebihara A, Kuramitsu S, Shinkai A, Shiro Y, Yokoyama 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-188812 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable thymidylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 213 amino acids
Theoretical weight: 24.73 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q970Q8 (Residues: 1-213; Coverage: 100%)
Gene names: STK_15430, tmk
Sequence domains: Thymidylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

9 bound ligands:
Ligand CL 2 x CL
Ligand PO4 1 x PO4
Ligand 1PE 3 x 1PE
Ligand PGE 3 x PGE
Ligand EDO 6 x EDO
Ligand DTT 1 x DTT
Ligand EPE 1 x EPE
Ligand PEG 11 x PEG
Ligand PG4 1 x PG4
1 modified residue:
Ligand MSE 4 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P212121
Unit cell:
a: 49.523Å b: 62.873Å c: 137.332Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.185 0.209
Expression system: Escherichia coli

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