+Open data
-Basic information
Entry | Database: PDB / ID: 7vkh | ||||||
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Title | Crystal structure of AF9 YEATS domain in complex with hit 2 | ||||||
Components | Protein AF-9 | ||||||
Keywords | TRANSCRIPTION / complex / inhibitor | ||||||
Function / homology | Function and homology information modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events ...modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / negative regulation of canonical Wnt signaling pathway / chromosome / gene expression / histone binding / molecular adaptor activity / chromatin binding / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Liu, Y. / Ruan, K. | ||||||
Funding support | China, 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Fragment-Based Discovery of AF9 YEATS Domain Inhibitors. Authors: Liu, Y. / Jin, R. / Lu, H. / Bian, K. / Wang, R. / Wang, L. / Gao, R. / Zhang, J. / Wu, J. / Yao, X. / Liu, X. / Liu, D. / Wang, X. / Zhang, Z. / Ruan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vkh.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vkh.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 7vkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/7vkh ftp://data.pdbj.org/pub/pdb/validation_reports/vk/7vkh | HTTPS FTP |
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-Related structure data
Related structure data | 7vkgC 4tmpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16328.885 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42568 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v PEGMME 2000, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9774 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→40 Å / Num. obs: 13767 / % possible obs: 97.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.14 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.26 |
Reflection shell | Resolution: 2.25→2.29 Å / Rmerge(I) obs: 0.381 / Num. unique obs: 13767 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TMP Resolution: 2.25→31.65 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 25.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.98 Å2 / Biso mean: 28.2108 Å2 / Biso min: 15.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→31.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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