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

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Basic information

Entry
Database: PDB / ID: 29tm
TitleKAT8 MUTANT (KAT6A SURROGATE, MYST-CRYST) IN COMPLEX WITH KAT6A INHIBITOR BAY-7728
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
: / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
AAA: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1565
Polymers32,5451
Non-polymers6114
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-8 kcal/mol
Surface area14270 Å2
Unit cell
Length a, b, c (Å)46.150, 59.169, 119.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules AAA

#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) (KAT6A numbering): 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 , 5 types, 305 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1J4O / 6-(azetidin-1-yl)-~{N}-(2-ethoxyphenyl)sulfonyl-4-fluoranyl-1-benzofuran-2-carboxamide


Mass: 418.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19FN2O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
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: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→43.07 Å / Num. obs: 36622 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 30.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.085 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5688 / CC1/2: 0.695 / Rrim(I) all: 1.029 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Mar 15, 2019data reduction
pointless1.11.11data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.663 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.214 1831 5 %
Rwork0.1775 34790 -
all0.179 --
obs-36621 98.815 %
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: 33.195 Å2
Baniso -1Baniso -2Baniso -3
1--0.661 Å20 Å20 Å2
2---0.125 Å20 Å2
3---0.786 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 37 302 2592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132403
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152225
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.6693267
X-RAY DIFFRACTIONr_angle_other_deg1.4271.5875142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76522.541122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94615418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3721511
X-RAY DIFFRACTIONr_chiral_restr0.1040.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02549
X-RAY DIFFRACTIONr_nbd_refined0.2220.2435
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22031
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21127
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.215
X-RAY DIFFRACTIONr_nbd_other0.1770.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2150.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_mcbond_it2.8521.4361105
X-RAY DIFFRACTIONr_mcbond_other2.851.4291104
X-RAY DIFFRACTIONr_mcangle_it4.3483.1941383
X-RAY DIFFRACTIONr_mcangle_other4.3483.2071384
X-RAY DIFFRACTIONr_scbond_it4.321.8681298
X-RAY DIFFRACTIONr_scbond_other4.3181.8691299
X-RAY DIFFRACTIONr_scangle_it6.3733.9471875
X-RAY DIFFRACTIONr_scangle_other6.3713.9511876
X-RAY DIFFRACTIONr_lrange_it10.09119.9572844
X-RAY DIFFRACTIONr_lrange_other10.09319.9682845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7420.3451270.3132424X-RAY DIFFRACTION94.5165
1.742-1.790.3021290.2782454X-RAY DIFFRACTION98.5126
1.79-1.8420.2921260.2542397X-RAY DIFFRACTION99.0966
1.842-1.8980.3021230.2432337X-RAY DIFFRACTION99.1936
1.898-1.9610.3081200.2512274X-RAY DIFFRACTION99.0484
1.961-2.0290.2351170.2112214X-RAY DIFFRACTION98.9809
2.029-2.1060.2511120.1822129X-RAY DIFFRACTION99.3351
2.106-2.1910.2121080.1822061X-RAY DIFFRACTION99.6783
2.191-2.2890.2261030.1981961X-RAY DIFFRACTION99.4699
2.289-2.40.2351000.1761892X-RAY DIFFRACTION99.1538
2.4-2.5290.247950.1681798X-RAY DIFFRACTION99.3179
2.529-2.6820.18900.1631717X-RAY DIFFRACTION99.2857
2.682-2.8670.202850.1611616X-RAY DIFFRACTION99.6485
2.867-3.0950.194800.1611514X-RAY DIFFRACTION99.5628
3.095-3.3890.182720.1671383X-RAY DIFFRACTION98.8451
3.389-3.7860.18670.1541274X-RAY DIFFRACTION99.1131
3.786-4.3660.168600.1311128X-RAY DIFFRACTION99
4.366-5.3330.168510.136974X-RAY DIFFRACTION99.1296
5.333-7.4850.262410.191779X-RAY DIFFRACTION99.1536
7.485-43.070.196250.184464X-RAY DIFFRACTION97.2167
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)
11.724-0.0446-0.79060.7184-0.30112.1262-0.0427-0.04820.04780.0579-0.017-0.0439-0.06780.09990.05970.01150.0009-0.00790.27770.00780.006619.171.76414.43
22.4617-2.1-1.58543.05341.44281.5251-0.1862-0.1832-0.28560.3256-0.03180.42740.219-0.0750.2180.1788-0.0120.05750.3914-0.0070.1036-0.23572.24735.181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA507 - 679
2X-RAY DIFFRACTION2ALLAAA680 - 778

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