The crystal structure of thymidylate kinase from pseudomonas aeruginosa PAO1 in complex with ADP,TMP and mg.

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).

Ligands and binding sites

• TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
• ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · chains A
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
• EDO · 1,2-ethanediol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1187 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

• 4EDH · The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9HZN8 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q9HZN8) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9HZN8
• Elsewhere: RCSB PDB 4EDH · PDBe 4EDH · UniProt Q9HZN8