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- PDB-22tg: Crystal Structure of MYST histone acetyltransferase KAT6A in comp... -

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Basic information

Entry
Database: PDB / ID: 22tg
TitleCrystal Structure of MYST histone acetyltransferase KAT6A in complex with Compound 20
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSCRIPTION / Kat6A / Inhibitor / Small molecule / Drug discovery / Acetyltransferase
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / regulation of mitochondrial transcription / 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 / histone H4K16 acetyltransferase activity / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / regulation of mitochondrial transcription / 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 / oogenesis / negative regulation of type I interferon production / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / protein-lysine-acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / transcription initiation-coupled chromatin remodeling / regulation of autophagy / promoter-specific chromatin binding / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / 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: 2.4 Å
AuthorsNarasimhaRao, K. / Vijayshankar, N. / SumalathaRani, T. / Kalishankar, B. / Chandregowda, V. / Chandrasekar, A. / Susanta, S. / Raymond, A.N. / David, C.M.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: To Be Published
Title: Crystal Structure of MYST histone acetyltransferase KAT6A in complex with Compound 20
Authors: NarasimhaRao, K. / Vijayshankar, N. / SumalathaRani, T. / Kalishankar, B. / Chandregowda, V. / Chandrasekar, A. / Susanta, S. / Raymond, A.N. / David, C.M.
History
DepositionJan 22, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 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
C: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9784
Polymers69,0652
Non-polymers9132
Water2,180121
1
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9892
Polymers34,5331
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9892
Polymers34,5331
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.685, 46.405, 120.922
Angle α, β, γ (deg.)90.000, 90.021, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / MYST-1 / Males-absent on ...Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / MYST-1 / Males-absent on the first protein homolog / hMOF / Protein acetyltransferase KAT8 / Protein propionyltransferase KAT8


Mass: 34532.727 Da / Num. of mol.: 2 / Fragment: BD1 domain
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, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-A1MDU / 2,6-dimethoxy-~{N}-[4-(pyrazol-1-ylmethyl)-2,3-dihydrofuro[2,3-e][1,2]benzoxazol-8-yl]benzenesulfonamide


Mass: 456.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H20N4O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.4 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M Sod. Malonate, pH 6.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→46.4 Å / Num. obs: 26843 / % possible obs: 98.2 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Net I/σ(I): 6
Reflection shellResolution: 2.36→2.45 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 2587 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
CrystFELdata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CT2

6ct2


Resolution: 2.4→43.324 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.789 / SU B: 17.747 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R: 0.595 / ESU R Free: 0.391
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.3725 1320 5.156 %RANDOM
Rwork0.2927 24280 --
all0.297 ---
obs-25600 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.507 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0 Å2-0.002 Å2
2---0.025 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 64 121 4450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124458
X-RAY DIFFRACTIONr_bond_other_d0.0020.0240
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.6726039
X-RAY DIFFRACTIONr_angle_other_deg1.343386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8585508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.126516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.55610772
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.82110198
X-RAY DIFFRACTIONr_chiral_restr0.1240.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023318
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0218
X-RAY DIFFRACTIONr_nbd_refined0.2530.21905
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2270.249
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22932
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2890.2202
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2950.215
X-RAY DIFFRACTIONr_mcbond_it2.9063.1082053
X-RAY DIFFRACTIONr_mcangle_it4.5815.5712554
X-RAY DIFFRACTIONr_scbond_it3.6453.3612405
X-RAY DIFFRACTIONr_scbond_other3.6443.3612406
X-RAY DIFFRACTIONr_scangle_it5.7766.0813485
X-RAY DIFFRACTIONr_scangle_other5.7766.083486
X-RAY DIFFRACTIONr_lrange_it8.69236.4246829
X-RAY DIFFRACTIONr_lrange_other8.69236.4346825
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.604950.59417640.59419010.5440.61897.79060.588
2.462-2.5290.561760.5117310.51218210.7980.8599.23120.467
2.529-2.6020.546790.45517080.45918190.8270.90798.24080.39
2.602-2.6820.551680.3816640.38717560.8270.92498.63330.327
2.682-2.770.422900.32415620.32816810.8610.93798.27480.271
2.77-2.8660.399800.30115350.30616340.8930.93898.83720.273
2.866-2.9740.436850.28514670.29215750.8510.95198.53970.261
2.974-3.0950.369770.28714520.29115400.8960.95299.28570.267
3.095-3.2320.439800.3113750.31614610.8870.95699.58930.293
3.232-3.3890.363890.28112660.28513650.9250.9799.26740.273
3.389-3.5710.31600.28113000.28213740.9590.97498.98110.271
3.571-3.7860.319730.25211670.25612480.9390.97499.3590.242
3.786-4.0450.307620.21211170.21711910.9390.97398.99240.205
4.045-4.3660.234640.20310260.20511040.9650.97298.73190.204
4.366-4.7780.322620.2019620.20810430.9580.97498.17830.198
4.778-5.3330.368620.2348790.2429510.9440.97198.94850.228
5.333-6.1430.34380.3017660.3048130.9520.95798.8930.291
6.143-7.4860.421300.3276980.3317360.9260.95598.9130.321
7.486-10.4320.442310.2985140.3055510.9270.95598.91110.324
10.432-43.3240.344190.3493260.3493540.9630.92697.45760.392

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