X-ray crystal structure at 1.61A resolution of human mitochondrial branched chain aminotransferase (bcatm) complexed with a biphenyl pyrrolidine ether compound and an internal aldimine linked plp cofactor.

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).

Ligands and binding sites

• PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
• EL1 · 3-({(3R)-1-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}oxy)-N-methyl-2'-[(methylsulfonyl)amino]biphenyl-4-carboxamide · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · chains 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, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2341 Ų buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

• 5CR5 · X-ray crystal structure at 1.61A resolution of human mitochondrial branched chain… · the same entry in another collection · chain A against A, TM-score 1.00
• O15382 · AlphaFold monomer V2.0 prediction for branched-chain-amino-acid aminotransferase… · 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 O15382
• Elsewhere: RCSB PDB 5CR5 · PDBe 5CR5 · UniProt O15382