Crystal strucutre of AF9 yeats domain in complex with a cyclopeptide inhibitor

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 50% strand (DSSP).

Ligands and binding sites

• EDX · (2~{S})-6-carbamimidamido-2-(phenylmethoxycarbonylamino)hexanoic acid · ligand · chains A, C
• EE0 · (2~{R})-2-azanylpentanoic acid · ligand · chains A, C
• EE3 · (2~{S})-2-azanyl-6-(1,3-oxazol-5-ylcarbonylamino) hexanoic acid · ligand · chains A, C
• NH2 · Amino group · ion · 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–C · 138 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).

Compared structures

• 6L5Z · Crystal strucutre of AF9 YEATS domain in complex with a cyclopeptide inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• P42568 · AlphaFold monomer V2.0 prediction for protein af-9 (P42568) · 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 P42568
• Elsewhere: RCSB PDB 6L5Z · PDBe 6L5Z · UniProt P42568