Crystal structure of dtmp kinase (ST1543) from sulfolobus tokodaii STRAIN7

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).

Ligands and binding sites

• CL · Chloride ion · ion · 2 copies · chains A
• PO4 · Phosphate ion · ion · chains A
• PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
• 1PE · Pentaethylene glycol · additive · 3 copies · chains A, B
• PGE · Triethylene glycol · additive · 3 copies · chains A
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
• PG4 · Tetraethylene glycol · 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 · 1122 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (engineered).

Compared structures

• 2PLR · Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7 · the same entry in another collection · chain B against B, TM-score 1.00
• Q970Q8 · AlphaFold monomer V2.0 prediction for probable thymidylate kinase (Q970Q8) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q970Q8
• Elsewhere: RCSB PDB 2PLR · PDBe 2PLR · UniProt Q970Q8