› 5yyf

X-ray diffraction
1.9Å resolution

Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group

Released:
DOI: 10.2210/pdb5yyf/pdb
PDB entry 5yyf coloured by chain, front view.
PDB entry 5yyf coloured by chain, side view.
PDB entry 5yyf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking.
Li X, Li XM, Jiang Y, Liu Z, Cui Y, Fung KY, van der Beelen SHE, Tian G, Wan L, Shi X, Allis CD, Li H, Li Y, Li XD
Nat Chem Biol 14 1140-1149 (2018)
PMID: 30374167

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154675 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein AF-9 Chains: A, C
Molecule details ›
Chains: A, C
Length: 141 amino acids
Theoretical weight: 16.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42568 (Residues: 1-138; Coverage: 24%)
Gene names: AF9, MLLT3, YEATS3
Sequence domains: YEATS family
Structure domains: YEATS domain
Peptide inhibitor PHQ-H3(Q5-K9) Chains: B, D
Molecule details ›
Chains: B, D
Length: 7 amino acids
Theoretical weight: 755 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 3 x SO4
Ligand FOA 2 x FOA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2
Unit cell:
a: 91.536Å b: 43.992Å c: 89.053Å
α: 90° β: 95.86° γ: 90°
R-values:
R R work R free
0.203 0.202 0.224
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

19 review citations

Epigenetic modifications of histones in cancer.
Zhao et al. (2019)
18 more

2 mentions without citation

Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins.
Li et al. (2021)
1 more