6L5Z: Crystal strucutre of AF9 YEATS domain

Crystal strucutre of AF9 YEATS domain in complex with a cyclopeptide inhibitor. Determined by X-ray diffraction at 3.05 Å resolution. Released 28 Oct 2020.

Method: X-ray diffraction
Resolution: 3.05 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,207
Mol. weight: 17.43 kDa
Released: 28 Oct 2020

Explore 6L5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L5Z contains 5 α-helices and 10 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-19	14	1
β-strand	30-37	8	1
α-helix	39-41	3
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	80	1	3
β-strand	81-89	9	2
β-strand	97-104	8	2
α-helix	107-108	2
α-helix	112-113	2
β-strand	114-125	12	1
α-helix	129-136	8

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A	protein	141	Homo sapiens	P42568 (AlphaFold model)
SC0-alo-ala-SC3-SC4-NH2	C	protein	6	synthetic construct

Sequence of entity 1 (A), FASTA

>6L5Z_1 Protein AF-9 (chains A)
GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHE
SFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHL
RCEKLTFNNPTEDFRRKLLKA

Sequence of entity 2 (C), FASTA

>6L5Z_2 SC0-ALO-ALA-SC3-SC4-NH2 (chains C)
XTAXXX

Primary citation

Selective Targeting of AF9 YEATS Domain by Cyclopeptide Inhibitors with Preorganized Conformation. Jiang, Y., Chen, G., Li, X.M. et al. J Am Chem Soc (2020) 142:21450-21459. DOI 10.1021/jacs.0c10324 · 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
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

Browse structure collections

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