Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor pb-pmtmu

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 15% strand (DSSP).

Ligands and binding sites

• EJ8 · [(2~{R},4~{A}~{R},6~{R},7~{A}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl) pyrimidin-1-yl]-2-phenyl-4~{A},6,7,7~{A}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid · ligand · chains A
• MG · Magnesium ion · metal · chains A
• GOL · Glycerol · additive · 2 copies · chains A
• BME · Beta-mercaptoethanol · additive · chains A

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

Pockets

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

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

• 6G2L · 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 6G2L · PDBe 6G2L · UniProt Q9NPB1