Structure of the enzyme-product complex resulting from tdg action on a G/HMU mismatch

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 12% strand (DSSP).

Ligands and binding sites

• ORP · 2-deoxy-5-phosphono-ribose · ligand · chains A, D
• ACY · Acetic acid · additive · 3 copies · chains A
• EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

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

Interfaces

3 interfaces between chains.

• C–D · 1222 Ų buried · 127 hydrogen bonds · nucleic-nucleic
• A–D · 603 Ų buried · 18 hydrogen bonds · protein-nucleic
• A–C · 407 Ų buried · 5 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

• 4XEG · Structure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch · the same entry in another collection · chain A against A, TM-score 1.00
• Q13569 · AlphaFold monomer V2.0 prediction for G/T mismatch-specific thymine DNA glycosylase… · a predicted model of the same protein · chain A 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 Q13569
• Elsewhere: RCSB PDB 4XEG · PDBe 4XEG · UniProt Q13569