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- PDB-7vkg: Crystal structure of AF9 YEATS domain in complex with Compound 10 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vkg | ||||||
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Title | Crystal structure of AF9 YEATS domain in complex with Compound 10 | ||||||
![]() | Protein AF-9 | ||||||
![]() | TRANSCRIPTION / Complex / inhibitor | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, Y. / Ruan, K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.9 KB | Display | ![]() |
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PDB format | ![]() | 28.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 637.4 KB | Display | ![]() |
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Full document | ![]() | 637.5 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vkhC ![]() 4tmpS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16328.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-7IV / ~{ | ||||
#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→40 Å / Num. obs: 13843 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.53 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 20.44 |
Reflection shell | Resolution: 1.83→1.86 Å / Rmerge(I) obs: 0.652 / Num. unique obs: 13843 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TMP Resolution: 1.83→40 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.62 / 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: 73.1 Å2 / Biso mean: 26.6103 Å2 / Biso min: 13.28 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→40 Å
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LS refinement shell | Resolution: 1.83→1.95 Å
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