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Yorodumi- PDB-7zjp: Optimization of TEAD P-Site Binding Fragment Hit into In Vivo Act... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zjp | ||||||
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Title | Optimization of TEAD P-Site Binding Fragment Hit into In Vivo Active Lead MSC-4106 | ||||||
Components | Transcriptional enhancer factor TEF-1 | ||||||
Keywords | TRANSCRIPTION / IMMUNOGLOBULIN-LIKE FOLD / ACTIVATOR / DISEASE MUTATION / DNA-BINDING / NUCLEUS / PHOSPHOPROTEIN / TRANSCRIPTION REGULATION / TRANSCRIPTION-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly ...TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Freire, F. / Heinrich, T. / Petersson, C. / Schneider, R. / Garg, S. / Schwarz, D. / Gunera, J. / Seshire, A. / Koetzner, L. / Schlesiger, S. ...Freire, F. / Heinrich, T. / Petersson, C. / Schneider, R. / Garg, S. / Schwarz, D. / Gunera, J. / Seshire, A. / Koetzner, L. / Schlesiger, S. / Musil, D. / Schilke, H. / Doerfel, B. / Diehl, P. / Boepple, P. / Lemos, A.R. / Sousa, P.M.F. / Freire, F. / Bandeiras, T.M. / Carswell, E. / Pearson, N. / Sirohi, S. / Hooker, M. / Trivier, E. / Broome, R. / Balsiger, A. / Crowden, A. / Dillon, C. / Wienke, D. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Optimization of TEAD P-Site Binding Fragment Hit into In Vivo Active Lead MSC-4106 . Authors: Heinrich, T. / Peterson, C. / Schneider, R. / Garg, S. / Schwarz, D. / Gunera, J. / Seshire, A. / Kotzner, L. / Schlesiger, S. / Musil, D. / Schilke, H. / Doerfel, B. / Diehl, P. / Bopple, P. ...Authors: Heinrich, T. / Peterson, C. / Schneider, R. / Garg, S. / Schwarz, D. / Gunera, J. / Seshire, A. / Kotzner, L. / Schlesiger, S. / Musil, D. / Schilke, H. / Doerfel, B. / Diehl, P. / Bopple, P. / Lemos, A.R. / Sousa, P.M.F. / Freire, F. / Bandeiras, T.M. / Carswell, E. / Pearson, N. / Sirohi, S. / Hooker, M. / Trivier, E. / Broome, R. / Balsiger, A. / Crowden, A. / Dillon, C. / Wienke, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zjp.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zjp.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/7zjp ftp://data.pdbj.org/pub/pdb/validation_reports/zj/7zjp | HTTPS FTP |
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-Related structure data
Related structure data | 7zjqC 3kysS 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: 25460.971 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P28347 #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: 3.81 Å3/Da / Density % sol: 67.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.2 M Ammonium Sulfate 20 % w/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999909 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999909 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→83.8 Å / Num. obs: 30690 / % possible obs: 74.7 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.19→2.39 Å / Num. unique obs: 1535 / CC1/2: 0.566 / Rpim(I) all: 0.557 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KYS Resolution: 2.19→27.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.219 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.196
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Displacement parameters | Biso max: 140.94 Å2 / Biso mean: 60.09 Å2 / Biso min: 29.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.19→27.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.31 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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