Alpha-ketoglutarate-dependent dioxygenase alkb in complex with fe, akg and methylated DNA under anaerobic environment using ft-ssx methods

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 34% strand (DSSP).

Ligands and binding sites

• AKG · 2-oxoglutaric acid · ligand · chains A
• O5W · [(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] [(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A
• FE · Fe (III) ion · metal · chains A

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

Pockets

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

Compared structures

• 6Y0Q · Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe, AKG and methylated DNA… · the same entry in another collection · chain A against A, TM-score 1.00
• P05050 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent dioxygenase alkb… · 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 P05050
• Elsewhere: RCSB PDB 6Y0Q · PDBe 6Y0Q · UniProt P05050