Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2B) component in the branched-chain alpha-ketoacid dehydrogenase complex (bckdc), oxidized coenzyme a-bound form

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 26% strand (DSSP).

Ligands and binding sites

• CAO · Oxidized coenzyme A · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
• ACT · Acetate ion · additive · 20 copies · chains A, B, C, D, E, H, F, G

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• E–F · 1512 Ų buried · 20 hydrogen bonds · protein-protein
• A–C · 1492 Ų buried · 22 hydrogen bonds · protein-protein
• B–C · 1466 Ų buried · 21 hydrogen bonds · protein-protein
• D–E · 1462 Ų buried · 21 hydrogen bonds · protein-protein
• D–F · 1461 Ų buried · 23 hydrogen bonds · protein-protein

Compared structures

• 2II3 · Crystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component… · the same entry in another collection · chain H against H, TM-score 1.00
• P11181 · AlphaFold monomer V2.0 prediction for lipoamide acyltransferase component of… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P11181
• Elsewhere: RCSB PDB 2II3 · PDBe 2II3 · UniProt P11181