5YYF: AF9 YEATS domain

Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor "PHQ-H3(Q5-K9)" modified at K9 with 2-furancarboyl group. Determined by X-ray diffraction at 1.9 Å resolution. Released 7 Nov 2018.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,720
Mol. weight: 35.25 kDa
Ligands: FOA
Released: 7 Nov 2018

Explore 5YYF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YYF contains 6 α-helices and 20 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-19	14	1
β-strand	30-37	8	1
α-helix	39-41	3
β-strand	48-54	7	2
β-strand	63-66	4	2
β-strand	71-77	7	1
β-strand	80	1	3
β-strand	81-89	9	2
β-strand	97-104	8	2
α-helix	112-113	2
β-strand	114-125	12	1
α-helix	129-135	7

Chains B and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	3

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-19	14	4
β-strand	30-37	8	4
α-helix	39-41	3
β-strand	48-54	7	5
β-strand	63-66	4	5
β-strand	71-77	7	4
β-strand	80	1	6
β-strand	81-89	9	5
β-strand	97-104	8	5
α-helix	112-113	2
β-strand	114-125	12	4
α-helix	129-137	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A, C	protein	141	Homo sapiens	P42568 (AlphaFold model)
Peptide inhibitor PHQ-H3(Q5-K9)	B, D	protein	7	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>5YYF_1 Protein AF-9 (chains A, C)
GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHE
SFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHL
RCEKLTFNNPTEDFRRKLLKA

Sequence of entity 2 (B, D), FASTA

>5YYF_2 Peptide inhibitor PHQ-H3(Q5-K9) (chains B, D)
XQTARKX

Ligands and cofactors

ID	Name	Formula	Copies
FOA	2-furoic acid	C5 H4 O3	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure-guided development of YEATS domain inhibitors by targeting pi-pi-pi stacking. Li, X., Li, X.M., Jiang, Y. et al. Nat Chem Biol (2018) 14:1140-1149. DOI 10.1038/s41589-018-0144-y · PubMed

Other PDB entries of the same protein (UniProt P42568 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PJ7 1.26 Å, MLLT3 in complex with compound PFI-6
7VKG 1.83 Å, Crystal structure of AF9 YEATS domain in complex with Compound 10
6MIL 1.93 Å, Crystal structure of AF9 YEATS domain in complex with histone H3K9bu
7EIC 1.95 Å, Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide
7EID 2.0 Å, Crystal structure of AF9 YEATS domain in complex with H4K8acK12ac peptide
8TLX 2.1 Å, Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic…
9ARR 2.1 Å, Crystal structure of AF9 YEATS domain in complex with dicrotonylated at K1007 and K1014…
8TLW 2.11 Å, Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic…
6LS6 2.2 Å, Crystal Structure of YEATS domain of AF9 in complex with H3K9bz peptide
7VKH 2.25 Å, Crystal structure of AF9 YEATS domain in complex with hit 2
4TMP 2.3 Å, Crystal structure of AF9 YEATS bound to H3K9ac peptide
9ARO 2.3 Å, Crystal structure of AF9 YEATS domain in complex with acetylated at K1007 MOZ

Browse structure collections

About this viewer

MolViewer shows 5YYF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.