› 2yog

X-ray diffraction
1.5Å resolution

Plasmodium falciparum thymidylate kinase in complex with a (thio)urea- alpha-deoxythymidine inhibitor

Released:
DOI: 10.2210/pdb2yog/pdb
PDB entry 2yog coloured by chain, front view.
PDB entry 2yog coloured by chain, side view.
PDB entry 2yog coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Synthesis and evaluation of α-thymidine analogues as novel antimalarials.
Cui H, Carrero-Lérida J, Silva AP, Whittingham JL, Brannigan JA, Ruiz-Pérez LM, Read KD, Wilson KS, González-Pacanowska D, Gilbert IH
J Med Chem 55 10948-57 (2012)
PMID: 23240776

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184671 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 210 amino acids
Theoretical weight: 24.73 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8I4S1 (Residues: 1-210; Coverage: 100%)
Gene names: PF3D7_1251300, TMK, TMPK
Sequence domains: Thymidylate kinase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

1 bound ligand:
Ligand 74X 2 x 74X
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 49.06Å b: 58.79Å c: 71.71Å
α: 90° β: 95.78° γ: 90°
R-values:
R R work R free
0.185 0.182 0.233
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

Prospects for new antibiotics: a molecule-centered perspective.
Walsh et al. (2014)
2 more

12 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
11 more