Cytosolic malate dehydrogenase 1 (peroxide-treated)

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).

Ligands and binding sites

• PEO · Hydrogen peroxide · ligand · 11 copies · chains A, B, C
• NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
• ETX · 2-ethoxyethanol · ligand · chains A, B
• SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
• GOL · Glycerol · additive · 6 copies · chains A, B, C
• FMT · Formic acid · additive · 5 copies · chains A, B, C
• ACT · Acetate ion · additive · 3 copies · chains B
• EDO · 1,2-ethanediol · additive · 3 copies · chains B, C
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

2 interfaces between chains.

• A–B · 1903 Ų buried · 40 hydrogen bonds · protein-protein
• A–C · 698 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (nonstandard, oxidation).

Compared structures

• 5NUE · Cytosolic Malate Dehydrogenase 1 (peroxide-treated) · the same entry in another collection · chain A against A, TM-score 1.00
• P93819 · AlphaFold monomer V2.0 prediction for malate dehydrogenase 1, cytoplasmic (P93819) · a predicted model of the same protein · chain C 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 P93819
• Elsewhere: RCSB PDB 5NUE · PDBe 5NUE · UniProt P93819