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- PDB-9ooh: Crystal structure of MYST acetyltransferase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9ooh
TitleCrystal structure of MYST acetyltransferase domain in complex with inhibitor 10b
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE/INHIBITOR / Acetyltransferase / Inhibitor / Complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / dosage compensation by inactivation of X chromosome / post-embryonic hemopoiesis / myeloid cell differentiation / NSL complex / negative regulation of epithelial to mesenchymal transition / negative regulation of type I interferon production / oogenesis / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / protein-lysine-acetyltransferase activity / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / neurogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / kinetochore / regulation of autophagy / nuclear matrix / HATs acetylate histones / chromosome / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain ...: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHermans, S.J. / Suwandi, A. / Parker, M.W. / Baell, J.B.
Funding support Australia, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1030704 Australia
National Health and Medical Research Council (NHMRC, Australia)1080146 Australia
National Health and Medical Research Council (NHMRC, Australia)1117602 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1194263 Australia
CitationJournal: J.Med.Chem. / Year: 2026
Title: Biological Activity and Structural Biology of Current KAT6A Inhibitor Chemotypes.
Authors: Suwandi, A. / Jin, J. / Zhao, Y. / Mudududdla, R. / Gee, Y.S. / Deora, G.S. / Sun, Y. / Wei, H. / Huang, F. / He, J.S. / George, A.J. / Hermans, S.J. / Leaver, D.J. / Parker, M.W. / Baell, J.B.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1176
Polymers34,4341
Non-polymers6835
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.665, 57.154, 120.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 34433.598 Da / Num. of mol.: 1 / Mutation: A142S, L145M, T146I, K157R, S204W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7Z6, histone acetyltransferase

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Non-polymers , 5 types, 133 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A1CDF / 5-ethoxy-2-fluoro-N'-[3-(2-hydroxyethoxy)benzene-1-sulfonyl]benzohydrazide


Mass: 398.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19FN2O6S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH7.5, 0.2-0.3 M NaCl, 12.5-15% PEG3350
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953729987144 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953729987144 Å / Relative weight: 1
ReflectionResolution: 2.05→41.39 Å / Num. obs: 20798 / % possible obs: 99.14 % / Redundancy: 9.8 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1257 / Rpim(I) all: 0.0429 / Rrim(I) all: 0.1331 / Net I/σ(I): 13.32
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.6835 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 2033 / CC1/2: 0.909 / CC star: 0.976 / Rpim(I) all: 0.2253 / Rrim(I) all: 0.7209 / % possible all: 99.36

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1496refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→41.387 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1004 4.86 %
Rwork0.1989 --
obs0.2012 20652 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→41.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 41 128 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072301
X-RAY DIFFRACTIONf_angle_d0.9093116
X-RAY DIFFRACTIONf_dihedral_angle_d7.9941361
X-RAY DIFFRACTIONf_chiral_restr0.058324
X-RAY DIFFRACTIONf_plane_restr0.005388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.15820.29621450.24362729X-RAY DIFFRACTION100
2.1582-2.29340.30721550.232776X-RAY DIFFRACTION99
2.2934-2.47040.2681350.2312794X-RAY DIFFRACTION100
2.4704-2.7190.28151310.22262807X-RAY DIFFRACTION100
2.719-3.11230.27021550.2052772X-RAY DIFFRACTION99
3.1123-3.92070.18711300.1782857X-RAY DIFFRACTION99
3.9207-41.3870.23781530.17752913X-RAY DIFFRACTION98

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