Ecmend-thdp-MN2+ complex soaked with 2-ketoglutarate for 21 S

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Ligands and binding sites

• TD6 · (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
• MN · Manganese (II) ion · metal · 9 copies · chains A, B, C, D, E, F, G, H
• GOL · Glycerol · additive · 14 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Interfaces

15 interfaces between chains.

• A–B · 3536 Ų buried · 55 hydrogen bonds · protein-protein
• E–F · 3532 Ų buried · 53 hydrogen bonds · protein-protein
• G–H · 3521 Ų buried · 55 hydrogen bonds · protein-protein
• C–D · 3507 Ų buried · 51 hydrogen bonds · protein-protein
• F–H · 1616 Ų buried · 39 hydrogen bonds · protein-protein

Compared structures

• 5EJ7 · EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 21 s · the same entry in another collection · chain H against H, TM-score 1.00
• P17109 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · 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 P17109
• Elsewhere: RCSB PDB 5EJ7 · PDBe 5EJ7 · UniProt P17109