7VKH: AF9 YEATS domain

Crystal structure of AF9 YEATS domain in complex with hit 2. Determined by X-ray diffraction at 2.25 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,311
Mol. weight: 33.36 kDa
Ligands: 7IY
Released: 5 Oct 2022

Explore 7VKH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VKH contains 9 α-helices and 18 β-strands across 2 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: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	7-19	13	1
β-strand	30-37	8	1
α-helix	38	1
α-helix	44-46	3
β-strand	48-54	7	2
β-strand	63-66	4	2
β-strand	71-77	7	1
β-strand	81-89	9	2
β-strand	97-104	8	2
α-helix	107-108	2
β-strand	109	1	3
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-124	11	1
α-helix	129-137	9

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-19	14	1
β-strand	30-37	8	1
α-helix	44-46	3
β-strand	48-54	7	4
β-strand	63-66	4	4
β-strand	71-77	7	1
β-strand	81-89	9	4
β-strand	97-104	8	4
α-helix	107-108	2
α-helix	112-113	2
β-strand	114-125	12	1
α-helix	129-137	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A, B	protein	138	Homo sapiens	P42568 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7VKH_1 Protein AF-9 (chains A, B)
MASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFP
RPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHLRCE
KLTFNNPTEDFRRKLLKA

Ligands and cofactors

ID	Name	Formula	Copies
7IY	~{N}-(3-azanyl-4-chloranyl-phenyl)-2-methoxy-ethanamide	C9 H11 Cl N2 O2	2

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

Primary citation

Fragment-Based Discovery of AF9 YEATS Domain Inhibitors. Liu, Y., Jin, R., Lu, H. et al. Int J Mol Sci (2022) 23. DOI 10.3390/ijms23073893 · 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
5YYF 1.9 Å, Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor…
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
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 7VKH 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.