E. COLI malate dehydrogenase with the inhibitor 6DHNAD

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).

Ligands and binding sites

• 6V0 · [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1564 Ų buried · 26 hydrogen bonds · protein-protein

Compared structures

• 5KKA · E. coli malate dehydrogenase with the inhibitor 6DHNAD · the same entry in another collection · chain A against A, TM-score 1.00
• P61889 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (P61889) · a predicted model of the same protein · chain B 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 P61889
• Elsewhere: RCSB PDB 5KKA · PDBe 5KKA · UniProt P61889