Pandda analysis group deposition of models with modelled events (E.G. bound ligands) -- crystal structure of NUDT7 in complex with RK4-350

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 35% strand (DSSP).

Ligands and binding sites

• H1P · 1-(4'-fluoro[1,1'-biphenyl]-2-yl)-1,3-dihydro-2H-pyrrol-2-one · ligand · chains A
• ACT · Acetate ion · additive · 2 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 2 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 2 modified (hydroxylation, oxidation).

Compared structures

• 5QHE · PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)… · the same entry in another collection · chain A against A, TM-score 1.00
• P0C024 · AlphaFold monomer V2.0 prediction for peroxisomal coenzyme a diphosphatase NUDT7 (P0C024) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P0C024
• Elsewhere: RCSB PDB 5QHE · PDBe 5QHE · UniProt P0C024