+Open data
-Basic information
Entry | Database: PDB / ID: 8pj7 | ||||||
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Title | MLLT3 in complex with compound PFI-6 | ||||||
Components | Protein AF-9 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / 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: 1.26 Å | ||||||
Authors | Raux, B. / Diaz-Saez, L. / Huber, K.V.M. / Fedorov, O. / Owen, D.R. / Londregan, A.T. / Bountra, C. / Edwards, A. / Arrowsmith, C. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2023 Title: Discovery of PFI-6, a small-molecule chemical probe for the YEATS domain of MLLT1 and MLLT3. Authors: Raux, B. / Buchan, K.A. / Bennett, J. / Christott, T. / Dowling, M.S. / Farnie, G. / Fedorov, O. / Gamble, V. / Gileadi, C. / Giroud, C. / Huber, K.V.M. / Korczynska, M. / Limberakis, C. / ...Authors: Raux, B. / Buchan, K.A. / Bennett, J. / Christott, T. / Dowling, M.S. / Farnie, G. / Fedorov, O. / Gamble, V. / Gileadi, C. / Giroud, C. / Huber, K.V.M. / Korczynska, M. / Limberakis, C. / Narayanan, A. / Owen, D.R. / Saez, L.D. / Stock, I.A. / Londregan, A.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pj7.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pj7.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 8pj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/8pj7 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/8pj7 | HTTPS FTP |
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-Related structure data
Related structure data | 8pjiC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17458.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / References: UniProt: P42568 |
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-Non-polymers , 5 types, 113 molecules
#2: Chemical | ChemComp-ZJ9 / ~{ | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
-Details
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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH=7.0 150 mM AmSO4 Gradient 20-30% PEG3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→46 Å / Num. obs: 42219 / % possible obs: 99.78 % / Redundancy: 27.1 % / Rmerge(I) obs: 0.07432 / Rpim(I) all: 0.01379 / Rrim(I) all: 0.07564 / Net I/σ(I): 20.71 |
Reflection shell | Resolution: 1.26→1.305 Å / Rmerge(I) obs: 1.597 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 4068 / Rpim(I) all: 0.482 / Rsym value: 1.672 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.233 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.079 Å2
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Refinement step | Cycle: 1 / Resolution: 1.26→46 Å
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