Structure of a naegleria tet-like dioxygenase in complex with 5- methylcytosine DNA

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).

Ligands and binding sites

• OGA · N-oxalylglycine · ligand · chains A, C
• MN · Manganese (II) ion · metal · chains A
• SO4 · Sulfate ion · ion · 4 copies · chains A
• EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, B

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–C · 624 Ų buried · 15 hydrogen bonds · protein-nucleic
• B–C · 618 Ų buried · 54 hydrogen bonds · nucleic-nucleic
• A–B · 372 Ų buried · 4 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

• 4LT5 · Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA · the same entry in another collection · chain A against A, TM-score 1.00
• D2W6T1 · AlphaFold monomer V2.0 prediction for tet-like dioxygenase 1 (D2W6T1) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 D2W6T1
• Elsewhere: RCSB PDB 4LT5 · PDBe 4LT5 · UniProt D2W6T1