9DZN: KAT6A MYST domain

KAT6A MYST domain complexed with a H3K14-CoA bisubstrate inhibitor. Determined by X-ray diffraction at 1.72 Å resolution. Released 19 Feb 2025.

Method: X-ray diffraction
Resolution: 1.72 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,587
Mol. weight: 36.75 kDa
Ligands: ZN, CMC
Released: 19 Feb 2025

Explore 9DZN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DZN contains 12 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: 12 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	536-539	4	1
β-strand	546-547	2	1
α-helix	550-559	10
β-strand	569-573	5	2
β-strand	576-582	7	2
α-helix	587-598	12
β-strand	613-622	10	2
β-strand	625-635	11	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	682-684	3
α-helix	685-705	21
α-helix	713-720	8
β-strand	722	1	4
α-helix	724-733	10
β-strand	737-739	3	5
β-strand	744-746	3	5
α-helix	750-762	13
α-helix	771-773	3
β-strand	774	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3K14	C	protein	19	Homo sapiens	Q6NXT2 (AlphaFold model)
Histone acetyltransferase KAT6A	A	protein	286	Homo sapiens	Q92794 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9DZN_1 Histone H3K14 (chains C)
QTARKSTGGKAPRKQLATK

Sequence of entity 2 (A), FASTA

>9DZN_2 Histone acetyltransferase KAT6A (chains A)
GSPPDPQVRCPSVIEFGKYEIHTWYSSPYPQEYSRLPKLYLCEFCLKYMKSRTILQQHMK
KCGWFHPPANEIYRKNNISVFEVDGNVSTIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVL
TQNDVKGCHLVGYFSKEKHCQQKYNVSCIMILPQYQRKGYGRFLIDFSYLLSKREGQAGS
PEKPLSDLGRLSYMAYWKSVILECLYHQNDKQISIKKLSKLTGICPQDITSTLHHLRMLD
FRSDQFVIIRREKLIQDHMAKLQLNLRPVDVDPECLRWTPVIVSNS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
CMC	Carboxymethyl coenzyme *a	C23 H38 N7 O18 P3 S	1

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

Primary citation

Modulation of the substrate preference of a MYST acetyltransferase by a scaffold protein. Sengupta, R.N., Brodsky, O., Bingham, P. et al. J Biol Chem (2025) 301:108262-108262. DOI 10.1016/j.jbc.2025.108262 · PubMed

Other PDB entries of the same protein (UniProt Q6NXT2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8T4R 1.2 Å, RAG2-PHD finger in complex with H3K4tBuNle peptide
8VLF 1.34 Å, Crystal structure of Ash1L PHD finger in complex with histone H3K4me3
2PUY 1.43 Å, Crystal Structure of the BHC80 PHD finger
9C0O 1.53 Å, Crystal structure of DmCfp1 PHD finger bound to H3K4me3
6OI3 1.66 Å, Crystal structure of human WDR5 in complex with monomethyl H3R2 peptide
7TRL 1.74 Å, Crystal structure of human BIRC2 BIR3 domain in complex with histone H3
8VLD 1.92 Å, Crystal structure of Ash1L PHD finger in complex with histone H3K4me2
5BWN 1.94 Å, Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine
9V5M 2.1 Å, The crystal structure of RBBP4-H3 complex
3KV4 2.19 Å, Structure of PHF8 in complex with histone H3
7W67 2.19 Å, The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with…
8SR6 2.22 Å, Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone…

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