Complex structure of the HRP3 pwwp domain with a 16-bp ta-rich DNA

Structure

x-ray diffraction · 5 distinct chains · 21% helix, 22% strand (DSSP).

Ligands and binding sites

• MLA · Malonic acid · additive · 3 copies · chains A, B, C
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, C

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

Pockets

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

Interfaces

9 interfaces between chains.

• F–G · 436 Ų buried · 37 hydrogen bonds · nucleic-nucleic
• A–B · 428 Ų buried · 3 hydrogen bonds · protein-protein
• B–F · 236 Ų buried · 4 hydrogen bonds · protein-nucleic
• D–E · 222 Ų buried · 19 hydrogen bonds · nucleic-nucleic
• A–E · 187 Ų buried · 3 hydrogen bonds · protein-nucleic

Compared structures

• 6IIQ · Complex structure of the HRP3 PWWP domain with a 16-bp TA-rich DNA · the same entry in another collection · chain G against G, TM-score 1.00
• Q9Y3E1 · AlphaFold monomer V2.0 prediction for hepatoma-derived growth factor- related protein 3… · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q9Y3E1
• Elsewhere: RCSB PDB 6IIQ · PDBe 6IIQ · UniProt Q9Y3E1