NMR solution structure of the phd domain from the yeast YNG1 protein in complex with H3(1-9)K4ME3 peptide

Structure

solution nmr · 2 distinct chains · 12% helix, 12% strand (DSSP).

Ligands and binding sites

• ZN · Zinc ion · metal · 2 copies · chains A

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

Interfaces

1 interface between chains.

• A–P · 598 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 1 modified (disulfide, methylation).

Compared structures

• 2JMJ · NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
• Q08465 · AlphaFold monomer V2.0 prediction for protein YNG1 (Q08465) · a predicted model of the same protein · chain A against A, TM-score 0.62
• P61830 · AlphaFold monomer V2.0 prediction for histone H3 (P61830) · a predicted model of the same protein · chain P against A, TM-score 0.35

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 Q08465
• Every structure of UniProt P61830
• Elsewhere: RCSB PDB 2JMJ · PDBe 2JMJ · UniProt Q08465 · UniProt P61830