PDB-29uq: KAT6A SURFACE MUTANT IN COMPLEX WITH CO-FACTOR ACETYL-CO-A

ID or keywords:

Entry

Database: PDB / ID: 29uq

Title

KAT6A SURFACE MUTANT IN COMPLEX WITH CO-FACTOR ACETYL-CO-A

Components

Histone acetyltransferase KAT6A

Keywords

TRANSFERASE / SURFACE MUTATION / HISTONE ACETYLTRANSFERASE / TRANSCRIPTION

Function / homology

Function and homology information

histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3 acetyltransferase activity / myeloid cell differentiation / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.134 Å

Authors

Hillig, R.C. / Puetter, V.

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2026
Title: KAT6A-inhibitor co-crystal structures: tackling a challenging crystallization target via two alternative approaches.
Authors: Puetter, V. / Bouche, L. / Nowak-Reppel, K. / Ferrara, S.J. / Gradl, S.N. / Korr, D. / Strathdee, C.A. / Ter Laak, A. / Hillig, R.C.

History

Deposition	Apr 9, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 9, 2026	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2026	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	29uq.cif.gz	448.1 KB	Display	PDBx/mmCIF format
PDB format	pdb29uq.ent.gz		Display	PDB format
PDBx/mmJSON format	29uq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/9u/29uq ftp://data.pdbj.org/pub/pdb/validation_reports/9u/29uq	HTTPS FTP

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Related structure data

Related structure data	29tmC 29tnC 29urC 29usC 29utC 29uuC 9fkr C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (2) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #67 - Jul 2005 TATA-Binding Protein similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#122 - Feb 2010
Enhanceosome
similarity (2)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#97 - Jan 2008
Circadian Clock Proteins
similarity (1)

Deposited unit

AAA: Histone acetyltransferase KAT6A

BBB: Histone acetyltransferase KAT6A

CCC: Histone acetyltransferase KAT6A

DDD: Histone acetyltransferase KAT6A

hetero molecules

133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Histone acetyltransferase KAT6A

hetero molecules

defined by author
33.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Histone acetyltransferase KAT6A

hetero molecules

defined by author
33.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

CCC: Histone acetyltransferase KAT6A

hetero molecules

defined by author
33.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

DDD: Histone acetyltransferase KAT6A

hetero molecules

defined by author
33.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	37.298, 64.587, 115.622
Angle α, β, γ (deg.)	85.607, 85.180, 89.607
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	TRP	TRP	AAA	A	509 - 776	3 - 270
2	2	1	PRO	PRO	TRP	TRP	BBB	B	509 - 776	3 - 270
3	3	2	PRO	PRO	PRO	PRO	AAA	A	509 - 778	3 - 272
4	4	2	PRO	PRO	PRO	PRO	CCC	C	509 - 778	3 - 272
5	5	3	PRO	PRO	ARG	ARG	AAA	A	509 - 775	3 - 269
6	6	3	PRO	PRO	ARG	ARG	DDD	D	509 - 775	3 - 269
7	7	4	PRO	PRO	THR	THR	BBB	B	509 - 777	3 - 271
8	8	4	PRO	PRO	THR	THR	CCC	C	509 - 777	3 - 271
9	9	5	PRO	PRO	ARG	ARG	BBB	B	509 - 775	3 - 269
10	10	5	PRO	PRO	ARG	ARG	DDD	D	509 - 775	3 - 269
11	11	6	SER	SER	TRP	TRP	CCC	C	508 - 776	2 - 270
12	12	6	SER	SER	TRP	TRP	DDD	D	508 - 776	2 - 270

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein	Histone acetyltransferase KAT6A / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt- ...MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt-related transcription factor-binding protein 2 / Zinc finger protein 220 Mass: 32173.229 Da / Num. of mol.: 4 / Mutation: C638S, C646S, C723S, C773S Source method: isolated from a genetically manipulated source Details: N-Terminal Gly-Ser: CLONING ARTIFACT, FROM THROMBIN CLEAVAGE SITE. ACETYLATION ON K604 (ALY): Post-translational Modification. Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6A, MOZ, MYST3, RUNXBP2, ZNF220 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92794, histone acetyltransferase

#1: Protein

Histone acetyltransferase KAT6A / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt- ...

Mass: 32173.229 Da / Num. of mol.: 4 / Mutation: C638S, C646S, C723S, C773S
Source method: isolated from a genetically manipulated source
Details: N-Terminal Gly-Ser: CLONING ARTIFACT, FROM THROMBIN CLEAVAGE SITE. ACETYLATION ON K604 (ALY): Post-translational Modification.
Source: (gene. exp.)

Homo sapiens (human) / Gene: KAT6A, MOZ, MYST3, RUNXBP2, ZNF220 / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92794, histone acetyltransferase

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Non-polymers , 5 types, 649 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S / Feature type*: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.8 % / Description: plates
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, sodium acetate, HEPES

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.13→44.59 Å / Num. obs: 54078 / % possible obs: 90.7 % / Redundancy: 2.1 % / B_iso Wilson estimate: 35.9 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.082 / R_rim(I) all: 0.11 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.13→2.26 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.463 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8587 / CC_1/2: 0.744 / R_rim(I) all: 0.626 / % possible all: 89.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	VERSION Jun 1, 2017	data reduction
pointless	1.10.18	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.134→44.588 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.906 / SU B: 16.267 / SU ML: 0.234 / Cross valid method: FREE R-VALUE / ESU R: 0.458 / ESU R Free: 0.27
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2754	2100	3.883 %
R_work	0.225	51976	-
all	0.227	-	-
obs	-	54076	90.716 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 37.386 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.355 Å²	0.252 Å²	1.562 Å²
2-	-	-2.472 Å²	-0.266 Å²
3-	-	-	0.334 Å²

Refinement step

Cycle: LAST / Resolution: 2.134→44.588 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8970	0	275	630	9875

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	9632
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	9063
X-RAY DIFFRACTION	r_angle_refined_deg	1.359	1.654	13045
X-RAY DIFFRACTION	r_angle_other_deg	1.119	1.578	20961
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.835	5	1110
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.209	21.677	507
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.181	15	1715
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.366	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	1183
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10529
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2263
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	1629
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	7907
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	4388
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	4265
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	537
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.093	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.191	0.2	66
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	168
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.26	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	1.276	0.744	4342
X-RAY DIFFRACTION	r_mcbond_other	1.256	0.743	4340
X-RAY DIFFRACTION	r_mcangle_it	2.164	1.66	5425
X-RAY DIFFRACTION	r_mcangle_other	2.165	1.66	5426
X-RAY DIFFRACTION	r_scbond_it	1.938	1.01	5290
X-RAY DIFFRACTION	r_scbond_other	1.939	1.011	5291
X-RAY DIFFRACTION	r_scangle_it	2.943	2.159	7601
X-RAY DIFFRACTION	r_scangle_other	2.943	2.161	7602
X-RAY DIFFRACTION	r_lrange_it	7.114	10.426	10565
X-RAY DIFFRACTION	r_lrange_other	7.072	9.992	10458
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	8655
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.079	0.05	8691
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.09	0.05	8673
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.1	0.05	8508
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.085	0.05	8686
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.092	0.05	8610

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.09827	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.09827	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.07948	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.07948	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.08989	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.08989	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.10024	0.05009
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.10024	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.08451	0.05009
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.08451	0.05009
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.09243	0.05009
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.09243	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.134-2.19	0.318	150	0.309	3712	0.31	4465	0.802	0.783	86.495	0.292
2.19-2.249	0.314	151	0.292	3732	0.293	4201	0.83	0.806	92.4304	0.267
2.249-2.315	0.339	150	0.28	3730	0.283	4244	0.813	0.847	91.4232	0.253
2.315-2.386	0.309	143	0.271	3536	0.272	3985	0.854	0.868	92.3212	0.24
2.386-2.464	0.294	140	0.26	3454	0.261	3972	0.858	0.883	90.4834	0.228
2.464-2.55	0.297	128	0.24	3166	0.242	3731	0.867	0.895	88.2873	0.207
2.55-2.646	0.315	126	0.25	3140	0.253	3731	0.858	0.877	87.5368	0.217
2.646-2.753	0.282	129	0.228	3183	0.23	3501	0.894	0.898	94.6015	0.199
2.753-2.875	0.302	126	0.22	3119	0.223	3436	0.876	0.911	94.4412	0.191
2.875-3.015	0.298	116	0.212	2861	0.215	3165	0.868	0.921	94.06	0.184
3.015-3.177	0.262	112	0.207	2783	0.209	3092	0.888	0.923	93.6287	0.184
3.177-3.369	0.272	104	0.204	2582	0.207	2936	0.914	0.931	91.485	0.188
3.369-3.6	0.216	93	0.203	2307	0.204	2721	0.93	0.937	88.2029	0.191
3.6-3.886	0.238	83	0.194	2042	0.196	2550	0.921	0.936	83.3333	0.183
3.886-4.254	0.249	84	0.182	2081	0.185	2339	0.926	0.946	92.5609	0.179
4.254-4.751	0.227	76	0.174	1871	0.176	2136	0.949	0.95	91.1517	0.178
4.751-5.475	0.257	66	0.216	1642	0.217	1874	0.91	0.919	91.1419	0.22
5.475-6.681	0.307	55	0.259	1370	0.26	1573	0.881	0.917	90.5912	0.258
6.681-9.344	0.294	42	0.233	1045	0.235	1263	0.911	0.921	86.0649	0.241
9.344-44.588	0.301	26	0.28	619	0.281	689	0.883	0.899	93.6139	0.302

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.3847	-0.582	0.5964	1.4312	-0.447	1.3039	-0.0277	-0.0073	0.0174	0.0828	-0.0023	-0.0345	-0.0223	-0.0386	0.03	0.044	0.0033	-0.0761	0.51	0.0709	0.2195	-8.118	-15.702	-29.358
2	0.9955	-1.3835	0.5608	3.1244	-1.1956	0.4793	0.1925	0.0729	-0.2336	-0.2292	-0.0426	0.3669	0.1265	0.1132	-0.1499	0.1801	0.0796	-0.1408	0.5328	0.0503	0.2161	-6.225	-43.593	-27.009
3	0.4527	-0.0881	1.0174	1.7625	-1.078	2.82	0.046	0.0165	-0.0315	-0.2738	-0.0587	0.0905	0.1276	0.1313	0.0127	0.1542	0.0195	-0.1178	0.5017	0.0362	0.2311	-13.06	-9.327	-57.847
4	0.8055	1.9488	-0.1977	5.8264	-1.8326	1.9958	-0.3006	0.0693	0.0943	-0.0026	-0.0289	0.1297	-1.1266	0.2827	0.3295	0.9259	-0.1443	-0.324	0.4837	0.1184	0.1998	-10.183	18.194	-62.487
5	0.1052	-0.1782	0.3379	1.6613	-0.1743	1.7061	-0.0065	-0.0176	-0.0616	0.1938	0.0023	-0.12	-0.0557	0.0193	0.0042	0.0576	-0.0183	-0.0948	0.5515	0.092	0.2379	-21.667	-11.975	27.677
6	0.4711	-0.6908	0.703	6.6533	-1.399	1.2795	0.2602	0.2339	-0.2478	0.4897	0.1286	-0.4414	0.4937	0.049	-0.3888	0.4318	0.0193	-0.2501	0.5216	-0.0528	0.4232	-19.083	-39.238	29.187
7	0.3116	0.2672	0.3096	1.4514	-0.7106	1.4199	0.0252	-0.0552	-0.0935	-0.1675	0.014	0.0141	0.0119	0.037	-0.0391	0.1091	-0.017	-0.0814	0.5226	0.0611	0.2017	-26.78	-4.38	-0.62
8	0.2645	1.1535	-0.226	5.1495	-1.0349	0.2387	0.0019	0.0273	0.0693	0.0465	0.0144	0.1503	-0.0745	0.0903	-0.0163	0.2499	-0.0529	-0.0321	0.4689	0.0521	0.2351	-24.919	23.767	-4.241

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	AAA	A	509 - 679	3 - 173
2	2	AAA	A	680 - 778	174 - 272
3	3	BBB	B	509 - 679	3 - 173
4	4	BBB	B	680 - 777	174 - 271
5	5	CCC	C	508 - 679	3 - 173
6	6	CCC	C	680 - 778	174 - 272
7	7	DDD	D	508 - 679	3 - 173
8	8	DDD	D	680 - 776	174 - 270

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Protein , 1 types, 4 molecules AAABBBCCCDDD

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Non-polymers , 5 types, 649 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Yorodumi