Crystal structure of the L136 aminotransferase K185A from acanthamoeba polyphaga mimivirus in the presence of the udp-viosamine external aldimine

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).

Ligands and binding sites

• Z7P · (2R,3R,4S,5S,6R)-3,4-dihydroxy-5-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-methyloxan-2-yl [(2R,3S,4R, 5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) · ligand · 4 copies · chains A, B, C, D
• NA · Sodium ion · metal · 2 copies · chains B, C, D
• CL · Chloride ion · ion · 8 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• C–D · 2299 Ų buried · 40 hydrogen bonds · protein-protein
• A–B · 2286 Ų buried · 41 hydrogen bonds · protein-protein
• A–D · 258 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 7MFP · crystal structure of the L136 aminotransferase K185A from acanthamoeba polyphaga… · the same entry in another collection · chain A 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 Q5UPL1
• Elsewhere: RCSB PDB 7MFP · PDBe 7MFP · UniProt Q5UPL1