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- PDB-8w13: Crystal structure of MYST acetyltransferase domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8w13
TitleCrystal structure of MYST acetyltransferase domain in complex with N-(1-(5-bromo-2-methoxyphenyl)-1H-1,2,3-triazol-4-yl)-2-methoxybenzenesulfonamide
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE / acetyltransferase / KAT8 / inhibitor
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 / protein-lysine-acetyltransferase activity / oogenesis / 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 / histone acetyltransferase / neurogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of autophagy / 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: 1.81 Å
AuthorsChen, C. / Dou, Y. / Wang, M. / Xu, C. / Buesking, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2024
Title: Identification of triazolyl KAT6 inhibitors via a templated fragment approach.
Authors: Chen, C. / Pawley, S.B. / Cote, J.M. / Carter, J. / Wang, M. / Xu, C. / Buesking, A.W.
History
DepositionFeb 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 25, 2024Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)33,85619
Polymers32,5451
Non-polymers1,31118
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.568, 58.989, 119.062
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 / hMOF


Mass: 32544.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus RIPL / References: UniProt: Q9H7Z6, histone acetyltransferase

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Non-polymers , 5 types, 235 molecules

#2: Chemical ChemComp-A1AEW / N-[(1M)-1-(5-bromo-2-methoxyphenyl)-1H-1,2,3-triazol-4-yl]-2-methoxybenzene-1-sulfonamide


Mass: 439.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15BrN4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7 / Details: 0.1M tris pH7.0,2M NaCl,0.22M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→46.57 Å / Num. obs: 30091 / % possible obs: 98.1 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 21.3
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1437 / CC1/2: 0.924 / Rpim(I) all: 0.233 / Rrim(I) all: 0.524 / % possible all: 81.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSFeb 5, 2021 BUILT=20210323data reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→43.41 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.385 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20352 1504 5 %RANDOM
Rwork0.16415 ---
obs0.16617 28532 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.105 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0 Å20 Å2
2--1.41 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.81→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 70 217 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152295
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.6683307
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5885314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91222.276123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29715425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6291512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022710
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02566
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_it1.3932.0241126
X-RAY DIFFRACTIONr_mcbond_other1.3872.0211125
X-RAY DIFFRACTIONr_mcangle_it2.2123.0211418
X-RAY DIFFRACTIONr_mcangle_other2.2113.0231419
X-RAY DIFFRACTIONr_scbond_it2.0162.3511321
X-RAY DIFFRACTIONr_scbond_other2.0152.3531322
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2083.3971890
X-RAY DIFFRACTIONr_long_range_B_refined5.71824.4192801
X-RAY DIFFRACTIONr_long_range_B_other5.60423.942759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 71 -
Rwork0.206 1717 -
obs--80.58 %
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)
11.44880.22240.10791.29961.16361.20240.0683-0.09620.00030.0673-0.09310.03360.07330.0110.02470.02980.00690.00740.06960.00430.011715.4113-17.5392-3.3359
21.84710.27951.41380.9878-0.88672.36440.0343-0.0978-0.0013-0.0395-0.0330.00540.0734-0.047-0.00130.01640.0031-0.00470.05490.02420.02325.0557-12.37090.0419
30.41450.06580.2760.6715-0.2991.1637-0.05680.05480.028-0.0105-0.011-0.0472-0.00150.11890.06780.01540.002-0.00090.05180.01090.016823.8841-8.866-17.8364
40.5681-0.12740.33770.2126-0.16240.279-0.00680.09970.00590.0442-0.0156-0.02010.02710.04820.02240.0806-0.00370.00860.0387-0.00630.020319.1365-15.1139-20.1117
50.23190.00180.12930.41420.08040.8101-0.03990.05970.01550.01260.02780.0445-0.0102-0.00750.0120.0318-0.01160.00690.05170.00610.022210.345-12.4934-24.271
62.4408-1.55732.30741.6607-2.94585.4652-0.0375-0.14250.3563-0.05130.0506-0.05960.1431-0.0877-0.01310.0147-0.0113-0.01390.0643-0.06090.11130.1655-12.5326-29.2205
72.91111.76911.73621.09961.03841.0553-0.21140.1940.2348-0.14870.07750.1683-0.10970.1530.13380.06680.0014-0.0410.1028-0.0090.0628-2.8955-17.5731-41.1088
84.43310.29571.56770.93620.66540.8985-0.22610.02080.2632-0.056-0.01030.241-0.1050.00710.23640.01340-0.0230.05530.0460.11151.8679-4.3742-31.0192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A177 - 198
2X-RAY DIFFRACTION2A199 - 229
3X-RAY DIFFRACTION3A230 - 269
4X-RAY DIFFRACTION4A270 - 316
5X-RAY DIFFRACTION5A317 - 354
6X-RAY DIFFRACTION6A355 - 375
7X-RAY DIFFRACTION7A376 - 418
8X-RAY DIFFRACTION8A419 - 448

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