Crystal structure of LSD2-npac with tranylcypromine

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).

Ligands and binding sites

• FA9 · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(3R,3aS,7aR)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate · ligand · chains A
• ZN · Zinc ion · metal · 3 copies · chains A

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 938 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 4GUU · Crystal structure of LSD2-NPAC with tranylcypromine · the same entry in another collection · chain A against A, TM-score 1.00
• Q8NB78 · AlphaFold monomer V2.0 prediction for lysine-specific histone demethylase 1B (Q8NB78) · a predicted model of the same protein · chain A against A, TM-score 0.99
• Q49A26 · AlphaFold monomer V2.0 prediction for putative oxidoreductase GLYR1 (Q49A26) · a predicted model of the same protein · chain B against A, TM-score 0.42

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 Q8NB78
• Every structure of UniProt Q49A26
• Elsewhere: RCSB PDB 4GUU · PDBe 4GUU · UniProt Q8NB78 · UniProt Q49A26