6PDG: MYST acetyltransferase domain

Crystal structure of MYST acetyltransferase domain in complex with inhibitor 83. Determined by X-ray diffraction at 1.92 Å resolution. Released 1 Apr 2020.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,400
Mol. weight: 32.71 kDa
Ligands: ZN, O9A
Released: 1 Apr 2020

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

Secondary structure: helices and β-sheets

6PDG contains 14 α-helices and 16 β-strands across 1 chain. 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: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	511-514	4	1
β-strand	517-520	4	1
α-helix	529-532	4
β-strand	537-539	3	1
β-strand	546-547	2	1
α-helix	550-559	10
β-strand	568-573	6	2
β-strand	576-582	7	2
α-helix	587-598	12
β-strand	613-621	9	2
β-strand	626-635	10	2
β-strand	642-644	3	3
β-strand	647-649	3	2
α-helix	651-653	3
α-helix	658-672	15
β-strand	677	1	4
β-strand	678-679	2	3
α-helix	680	1
α-helix	683-684	2
α-helix	685-704	20
α-helix	712-719	8
β-strand	721	1	4
α-helix	723-732	10
β-strand	736-739	4	5
β-strand	742-745	4	5
α-helix	749-757	9
α-helix	759-761	3
α-helix	764-765	2
α-helix	770-772	3
β-strand	773	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone acetyltransferase KAT8	A	protein	272	Homo sapiens	Q9H7Z6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6PDG_1 Histone acetyltransferase KAT8 (chains A)
KYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPP
GKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGA
HIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDL
GKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVIC
VTPKLVEEHLKSAQYKKPPITVDSVCLKWAPP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
O9A	5-ethoxy-2-fluoro-3-methyl-N'-[(naphthalen-2-yl)sulfonyl]benzohydrazide	C20 H19 F N2 O4 S	1

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

Primary citation

Discovery of Acylsulfonohydrazide-Derived Inhibitors of the Lysine Acetyltransferase, KAT6A, as Potent Senescence-Inducing Anti-Cancer Agents. Priebbenow, D.L., Leaver, D.J., Nguyen, N. et al. J Med Chem (2020) 63:4655-4684. DOI 10.1021/acs.jmedchem.9b02071 · PubMed

Other PDB entries of the same protein (UniProt Q9H7Z6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

29UU 1.3 Å, KAT8 mutant (KAT6A surrogate, myst-cryst) in complex with KAT6A inhibitor example-41
9OOA 1.39 Å, Crystal structure of MYST acetyltransferase domain in complex with inhibitor 7
29UT 1.4 Å, KAT8 mutant (KAT6A surrogate, myst-cryst) in complex with KAT6A inhibitor compound 2
2PQ8 1.45 Å, MYST histone acetyltransferase 1
9OOF 1.68 Å, Crystal structure of MYST acetyltransferase domain in complex with inhibitor 10e
29TM 1.7 Å, KAT8 mutant (KAT6A surrogate, myst-cryst) in complex with KAT6A inhibitor bay-7728
6OIN 1.7 Å, Crystal structure of MYST acetyltransferase domain in complex with inhibitor CTX-124143
6OIO 1.7 Å, Crystal structure of MYST acetyltransferase domain in complex with inhibitor 60
6OIQ 1.75 Å, Crystal structure of MYST acetyltransferase domain in complex with inhibitor 63
6OWI 1.75 Å, Crystal structure of MYST acetyltransferase domain in complex with inhibitor 85
5WCI 1.78 Å, Human MYST histone acetyltransferase 1
29TN 1.8 Å, KAT8 mutant (KAT6A surrogate, myst-cryst) in complex with KAT6A inhibitor compound 38

Browse structure collections

About this viewer

MolViewer shows 6PDG 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.