Molecular basis of histone H3K4ME3 recognition by ING4

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 23% strand (DSSP).

Ligands and binding sites

• ZN · Zinc ion · metal · 4 copies · chains A, C
• NA · Sodium ion · metal · chains A
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A
• DTU · (2R,3S)-1,4-dimercaptobutane-2,3-diol · additive · chains C

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• C–D · 732 Ų buried · 18 hydrogen bonds · protein-protein
• A–B · 546 Ų buried · 15 hydrogen bonds · protein-protein
• A–D · 195 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 85 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (additive adduct, methylation).

Compared structures

• 2VNF · Molecular basis of histone H3K4ME3 recognition by ING4 · the same entry in another collection · chain D against D, TM-score 1.00
• Q9UNL4 · AlphaFold monomer V2.0 prediction for inhibitor of growth protein 4 (Q9UNL4) · a predicted model of the same protein · chain A against A, TM-score 0.97
• Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain B against A, TM-score 0.65

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 Q9UNL4
• Every structure of UniProt Q5TEC6
• Elsewhere: RCSB PDB 2VNF · PDBe 2VNF · UniProt Q9UNL4 · UniProt Q5TEC6