Reaction intermediate structure of entamoeba histolytica methionine gamma-lyase 1 containing methionine imine-pyridoxamine-5'-phosphate and alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 16% strand (DSSP).

Ligands and binding sites

• 2LM · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid · ligand · 3 copies · chains B, C, A, D
• 4LM · (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid · ligand · chains A, D
• MEE · Methanethiol · ligand · chains A, D
• SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 2 copies · chains A, C

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–D · 2834 Ų buried · 40 hydrogen bonds · protein-protein
• B–C · 2789 Ų buried · 37 hydrogen bonds · protein-protein
• A–C · 1443 Ų buried · 27 hydrogen bonds · protein-protein
• B–D · 1411 Ų buried · 28 hydrogen bonds · protein-protein
• C–D · 949 Ų buried · 14 hydrogen bonds · protein-protein

Compared structures

• 3AEL · Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1… · the same entry in another collection · chain B against B, 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 Q86D28
• Elsewhere: RCSB PDB 3AEL · PDBe 3AEL · UniProt Q86D28