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- PDB-29tn: KAT8 MUTANT (KAT6A SURROGATE, MYST-CRYST) IN COMPLEX WITH KAT6A I... -

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Basic information

Entry
Database: PDB / ID: 29tn
TitleKAT8 MUTANT (KAT6A SURROGATE, MYST-CRYST) IN COMPLEX WITH KAT6A INHIBITOR COMPOUND 38
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE / SURROGATE / HISTONE ACETYLTRANSFERASE / TRANSCRIPTION / SMALL MOLECULE INHIBITOR
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / histone H4K16 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / NSL complex / protein propionyltransferase activity / myeloid cell differentiation / histone H4 acetyltransferase activity ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / histone H4K16 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / NSL complex / protein propionyltransferase activity / myeloid cell differentiation / histone H4 acetyltransferase activity / regulation of mRNA processing / post-embryonic hemopoiesis / dosage compensation by inactivation of X chromosome / oogenesis / negative regulation of epithelial to mesenchymal transition / Formation of WDR5-containing histone-modifying complexes / negative regulation of type I interferon production / histone acetyltransferase activity / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / neurogenesis / protein-lysine-acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / regulation of autophagy / kinetochore / nuclear matrix / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
: / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / RNA binding activity-knot of a chromodomain / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / 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 / RNA binding activity-knot of a chromodomain / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / 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
: / DI(HYDROXYETHYL)ETHER / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHillig, R.C. / Puetter, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
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.
#1: Journal: J.Med.Chem. / Year: 2024
Title: Discovery and Characterization of BAY-184: A New Potent and Selective Acylsulfonamide-Benzofuran In Vivo -Active KAT6AB Inhibitor.
Authors: Ter Laak, A. / Hillig, R.C. / Ferrara, S.J. / Korr, D. / Barak, N. / Lienau, P. / Herbert, S. / Fernandez-Montalvan, A.E. / Neuhaus, R. / Gorjanacz, M. / Puetter, V. / Badock, V. / Bone, W. ...Authors: Ter Laak, A. / Hillig, R.C. / Ferrara, S.J. / Korr, D. / Barak, N. / Lienau, P. / Herbert, S. / Fernandez-Montalvan, A.E. / Neuhaus, R. / Gorjanacz, M. / Puetter, V. / Badock, V. / Bone, W. / Strathdee, C. / Siegel, F. / Schatz, C. / Nowak-Reppel, K. / Doehr, O. / Gradl, S. / Hartung, I.V. / Meyerson, M. / Bouche, L.
History
DepositionApr 8, 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 KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,49711
Polymers32,5451
Non-polymers95210
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-41 kcal/mol
Surface area13740 Å2
Unit cell
Length a, b, c (Å)46.142, 57.426, 121.314
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 / 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: 32544.512 Da / Num. of mol.: 1 / Mutation: Y95H, A161S, L164M, T165I, K176R, T213S, I216N
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: KAT8, MOF, MYST1, PP7073 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H7Z6, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 7 types, 220 molecules

#2: Chemical ChemComp-A1J4N / 6-(dimethylamino)-~{N}-(2-ethoxy-5-propan-2-yl-phenyl)sulfonyl-1-benzofuran-2-carboxamide


Mass: 430.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG, HEPES

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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: May 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→46.11 Å / Num. obs: 30369 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.154 / Net I/σ(I): 9.9
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 6 % / Rmerge(I) obs: 1.529 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4755 / CC1/2: 0.529 / Rrim(I) all: 1.658 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSVERSION Mar 15, 2019data reduction
pointless1.11.11data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.496 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22095 1519 5 %RANDOM
Rwork0.17666 ---
obs0.17886 28850 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å2-0 Å2
2---2.53 Å20 Å2
3---1.74 Å2
Refinement stepCycle: 1 / Resolution: 1.8→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 55 210 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132382
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152236
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.6613238
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5885153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31821.885122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9911513
X-RAY DIFFRACTIONr_chiral_restr0.1040.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
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_it2.3761.1961086
X-RAY DIFFRACTIONr_mcbond_other2.3511.1911085
X-RAY DIFFRACTIONr_mcangle_it3.5322.6491359
X-RAY DIFFRACTIONr_mcangle_other3.5342.6571360
X-RAY DIFFRACTIONr_scbond_it5.7171296
X-RAY DIFFRACTIONr_scbond_other5.7151297
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7491870
X-RAY DIFFRACTIONr_long_range_B_refined9.5352763
X-RAY DIFFRACTIONr_long_range_B_other9.472710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å
RfactorNum. reflection% reflection
Rfree0.422 108 -
Rwork0.338 2046 -
obs--95.78 %
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)
11.31620.047-0.87040.6307-0.55781.9614-0.0503-0.03320.02230.0416-0.0028-0.0479-0.00410.09620.05310.0065-0.0064-0.00580.438-0.00510.00718.81969.21214.311
22.3214-1.568-0.90032.31551.32421.1607-0.2126-0.2755-0.27820.40830.05480.43110.16860.02970.15780.12350.02010.09730.49370.03370.102-0.13769.09535.085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A501 - 679
2X-RAY DIFFRACTION2A680 - 778

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