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- PDB-29ur: KAT6A SURFACE MUTANT IN COMPLEX WITH INHIBITOR WM-8014 -

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Basic information

Entry
Database: PDB / ID: 29ur
TitleKAT6A SURFACE MUTANT IN COMPLEX WITH INHIBITOR WM-8014
ComponentsHistone acetyltransferase KAT6A
KeywordsTRANSFERASE / SURFACE MUTATION / HISTONE ACETYLTRANSFERASE / TRANSCRIPTION / SMALL MOLECULE INHIBITOR COMPLEX
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
Chem-7KM / ACETYL COENZYME *A / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.784 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
AAA: Histone acetyltransferase KAT6A
BBB: Histone acetyltransferase KAT6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6716
Polymers64,3462
Non-polymers1,3254
Water82946
1
AAA: Histone acetyltransferase KAT6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0483
Polymers32,1731
Non-polymers8752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Histone acetyltransferase KAT6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6233
Polymers32,1731
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.212, 57.620, 62.541
Angle α, β, γ (deg.)94.073, 90.339, 103.220
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11AAA
21BBB

NCS domain segments:

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

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-7KM / 4-fluoro-5-methyl-N'-(phenylsulfonyl)[1,1'-biphenyl]-3-carbohydrazide


Mass: 384.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17FN2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.97 Å3/Da / Density % sol: 37.52 % / Description: plate-shaped crystals
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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.78→43.27 Å / Num. obs: 11480 / % possible obs: 93.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 59.9 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.156 / Rsym value: 0.133 / Net I/σ(I): 7.5
Reflection shellResolution: 2.78→2.95 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.99 / Num. unique obs: 1740 / CC1/2: 0.651 / Rrim(I) all: 1.283 / Rsym value: 1.093 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Jan 26, 2018 BUILT=20180126data reduction
pointlessversion 1.11.8data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.784→43.27 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.828 / SU B: 61.466 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.617
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3286 574 5.002 %
Rwork0.2778 10902 -
all0.28 --
obs-11476 93.453 %
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: 70.431 Å2
Baniso -1Baniso -2Baniso -3
1--2.461 Å2-2.48 Å2-1.046 Å2
2--1.435 Å2-1.12 Å2
3---2.244 Å2
Refinement stepCycle: LAST / Resolution: 2.784→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 80 46 4538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154380
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.6526312
X-RAY DIFFRACTIONr_angle_other_deg0.9671.57710118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9275531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.44321.762244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5815829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0531525
X-RAY DIFFRACTIONr_chiral_restr0.0340.2571
X-RAY DIFFRACTIONr_chiral_restr_other0.0720.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021103
X-RAY DIFFRACTIONr_nbd_refined0.1450.2954
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1510.24422
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22154
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2168
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.231
X-RAY DIFFRACTIONr_nbd_other0.1540.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.210
X-RAY DIFFRACTIONr_mcbond_it0.3733.2672125
X-RAY DIFFRACTIONr_mcbond_other0.3733.2672124
X-RAY DIFFRACTIONr_mcangle_it0.697.3422649
X-RAY DIFFRACTIONr_mcangle_other0.697.3422650
X-RAY DIFFRACTIONr_scbond_it0.3463.4212539
X-RAY DIFFRACTIONr_scbond_other0.3463.4222540
X-RAY DIFFRACTIONr_scangle_it0.617.6873661
X-RAY DIFFRACTIONr_scangle_other0.617.6883662
X-RAY DIFFRACTIONr_lrange_it2.88839.4225249
X-RAY DIFFRACTIONr_lrange_other2.87739.4085246
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.058904
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.090680.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.090680.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.784-2.8560.46360.434692X-RAY DIFFRACTION82.2599
2.856-2.9340.426430.411806X-RAY DIFFRACTION96.4773
2.934-3.0190.378420.352802X-RAY DIFFRACTION94.5129
3.019-3.1110.298380.343719X-RAY DIFFRACTION92.8834
3.111-3.2130.299360.305683X-RAY DIFFRACTION90.7828
3.213-3.3250.219380.291734X-RAY DIFFRACTION96.6208
3.325-3.4490.374350.286668X-RAY DIFFRACTION95.3867
3.449-3.5890.371360.276681X-RAY DIFFRACTION95.0928
3.589-3.7480.363320.293607X-RAY DIFFRACTION94.948
3.748-3.9290.339330.271616X-RAY DIFFRACTION95.022
3.929-4.140.368280.269544X-RAY DIFFRACTION90.3633
4.14-4.3880.268280.238524X-RAY DIFFRACTION93.2432
4.388-4.6880.259270.221517X-RAY DIFFRACTION96.4539
4.688-5.0590.286260.228487X-RAY DIFFRACTION96.4286
5.059-5.5340.379220.29429X-RAY DIFFRACTION94.1545
5.534-6.1740.312200.308377X-RAY DIFFRACTION89.819
6.174-7.1060.447190.299354X-RAY DIFFRACTION95.8869
7.106-8.6440.303150.245298X-RAY DIFFRACTION96.6049
8.644-11.9880.292120.208230X-RAY DIFFRACTION90.6367
11.988-43.270.28280.286134X-RAY DIFFRACTION97.931
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)
14.31281.1742-0.32195.53850.43364.09580.0263-0.1064-0.0371-0.02050.09750.1410.5405-0.0599-0.12380.0789-0.0021-0.06180.0399-0.06590.3981-10.176228.2921-15.7186
23.2892-2.0913-1.43663.75870.92443.1781-0.13541.08090.0281-1.06520.06090.09070.1283-0.56750.07451.0379-0.2253-0.06210.7014-0.0790.6445-8.502527.1947-42.6477
33.16090.1870.38494.27420.34594.20180.0379-0.17650.087-0.02950.07960.0577-0.43310.0577-0.11750.05370.0027-0.02880.0379-0.07320.4204-5.099456.0513-5.9562
40.76590.28942.23680.41621.15947.52550.0053-0.3068-0.04370.4643-0.0249-0.04540.2921-0.26960.01960.7646-0.0448-0.02190.6262-0.0180.5843-3.54754.969321.0187
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AAAA509 - 6863 - 180
22AAAA687 - 778181 - 272
33BBBB509 - 6863 - 180
44BBBB687 - 778181 - 272

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