Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor npb-T

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 15% strand (DSSP).

Ligands and binding sites

• 2JW · 1-{2-deoxy-3,5-O-[(4-nitrophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · chains A
• MG · Magnesium ion · metal · chains A
• PO4 · Phosphate ion · ion · chains A
• GOL · Glycerol · additive · 7 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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.

Compared structures

• 4NFL · Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9NPB1 · AlphaFold monomer V2.0 prediction for 5'(3')-deoxyribonucleotidase, mitochondrial (Q9NPB1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9NPB1
• Elsewhere: RCSB PDB 4NFL · PDBe 4NFL · UniProt Q9NPB1