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- PDB-29us: KAT6A SURFACE MUTANT IN COMPLEX WITH QUINOLINE INHIBITOR COMPOUND-1 -

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Basic information

Entry
Database: PDB / ID: 29us
TitleKAT6A SURFACE MUTANT IN COMPLEX WITH QUINOLINE INHIBITOR COMPOUND-1
ComponentsHistone acetyltransferase KAT6A
KeywordsTRANSFERASE / SURFACE MUTATION / HISTONE ACETYLTRANSFERASE / TRANSCRIPTION / SMALL MOLECULE INHIBITOR
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 ...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 / chromosome organization / acetyltransferase activity / histone acetyltransferase activity / protein-lysine-acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / regulation of signal transduction by p53 class mediator / PML body / cellular senescence / transcription coregulator activity / nucleosome / nucleosome assembly / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 ...: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHillig, R.C. / Puetter, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionApr 9, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2026Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT6A
B: Histone acetyltransferase KAT6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2966
Polymers64,3462
Non-polymers9504
Water66737
1
A: Histone acetyltransferase KAT6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6483
Polymers32,1731
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase KAT6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6483
Polymers32,1731
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.033, 58.910, 64.925
Angle α, β, γ (deg.)93.02, 91.25, 102.89
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 509 - 778 / Label seq-ID: 3 - 272

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#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.: 2 / Mutation: C638S, C646S, C723S, C773S
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL GS: 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1J4W / 6-(dimethylamino)-N-(2-methylquinolin-8-yl)sulfonyl-1-benzofuran-2-carboxamide


Mass: 409.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, sodium acetate, HEPES; glycerol as cryo protectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→44.25 Å / Num. obs: 13855 / % possible obs: 94.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 49.9 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.194 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.86 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2261 / CC1/2: 0.58 / Rrim(I) all: 0.58 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
pointless1.11.11data scaling
XDSVERSION Jan 26, 2018data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→34.19 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.863 / SU B: 42.529 / SU ML: 0.44 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3094 432 3.2 %RANDOM
Rwork0.2351 ---
obs0.23738 12969 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.095 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20.54 Å2-1.22 Å2
2--2.68 Å21.95 Å2
3----5.32 Å2
Refinement stepCycle: 1 / Resolution: 2.7→34.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 60 37 4609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194728
X-RAY DIFFRACTIONr_bond_other_d0.0030.024344
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.9816397
X-RAY DIFFRACTIONr_angle_other_deg1.0893.00310062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5775542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78423.455220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.53615846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1291526
X-RAY DIFFRACTIONr_chiral_restr0.1050.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02988
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9050.4822162
X-RAY DIFFRACTIONr_mcbond_other0.9050.4822161
X-RAY DIFFRACTIONr_mcangle_it1.5921.0782700
X-RAY DIFFRACTIONr_mcangle_other1.5921.0782701
X-RAY DIFFRACTIONr_scbond_it2.9020.6362566
X-RAY DIFFRACTIONr_scbond_other2.9090.6382567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8661.3863695
X-RAY DIFFRACTIONr_long_range_B_refined6.9316.2095355
X-RAY DIFFRACTIONr_long_range_B_other6.9266.2015353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17636 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 32 -
Rwork0.317 979 -
obs--95.74 %
Refinement TLS params.

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

IDL11 (°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)
12.81760.46920.20054.3801-0.31034.54870.0786-0.2237-0.13460.0197-0.00690.09420.4947-0.0279-0.07170.1141-0.01960.00930.0541-0.17411.0027-10.27629.11-15.766
21.749-0.1279-0.69181.10420.77437.97730.01120.8281-0.0736-0.9992-0.0432-0.00970.5420.14730.0321.11210.0640.02770.4421-0.19051.2179-7.45127.591-43.505
32.66330.82930.50624.04510.62854.1563-0.1005-0.09530.0658-0.0410.1176-0.1805-0.350.2619-0.01710.1053-0.03890.02660.0715-0.2161.0099-4.98756.877-6.856
40.5318-0.16010.81890.55391.031513.0989-0.2056-0.5784-0.11530.6879-0.0246-0.0956-0.2201-0.00550.23011.12-0.288-0.14771.0219-0.05631.4192-2.91456.37220.973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A509 - 679
2X-RAY DIFFRACTION2A680 - 778
3X-RAY DIFFRACTION3B509 - 679
4X-RAY DIFFRACTION4B680 - 778

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