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

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 17% strand (DSSP).

Ligands and binding sites

• O84 · [(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-[(~{E})-3-phosphonoprop-1-enyl]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 · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1191 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (artifact).

Compared structures

• 6G2N · Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
• Q8TCD5 · AlphaFold monomer V2.0 prediction for 5'(3')-deoxyribonucleotidase, cytosolic type… · 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 Q8TCD5
• Elsewhere: RCSB PDB 6G2N · PDBe 6G2N · UniProt Q8TCD5