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Yorodumi- PDB-4zql: Crystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphe... -
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-Basic information
Entry | Database: PDB / ID: 4zql | ||||||
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Title | Crystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)benzenesulfonamide inhibitor | ||||||
Components | Transcription intermediary factor 1-alpha | ||||||
Keywords | LIGASE / Transcriptional coactivator / histone H3 modifications / E3 protein-ubiquitin ligase activity / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / male germ cell nucleus / epithelial cell proliferation / regulation of signal transduction by p53 class mediator ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / calcium ion homeostasis / cellular response to estrogen stimulus / estrogen response element binding / Signaling by FGFR1 in disease / male germ cell nucleus / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / nuclear receptor binding / protein catabolic process / lysine-acetylated histone binding / euchromatin / RING-type E3 ubiquitin transferase / regulation of protein stability / response to peptide hormone / ubiquitin protein ligase activity / negative regulation of epithelial cell proliferation / Signaling by BRAF and RAF1 fusions / p53 binding / regulation of apoptotic process / transcription by RNA polymerase II / transcription coactivator activity / protein ubiquitination / protein kinase activity / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / mitochondrion / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Tallant, C. / Structural Genomics Consortium (SGC) / Clark, P.G.K. / Vieira, L.C.C. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. ...Tallant, C. / Structural Genomics Consortium (SGC) / Clark, P.G.K. / Vieira, L.C.C. / Krojer, T. / Nunez-Alonso, G. / Picaud, S. / Fedorov, O. / Dixon, D.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brennan, P.E. / Knapp, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of TRIM24 with 3,4-dimethoxy-N-(6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)benzenesulfonamide inhibitor Authors: Clark, P.G. / Vieira, L.C. / Tallant, C. / Fedorov, O. / Singleton, D.C. / Rogers, C.M. / Monteiro, O.P. / Bennett, J.M. / Baronio, R. / Muller, S. / Daniels, D.L. / Mendez, J. / Knapp, S. / ...Authors: Clark, P.G. / Vieira, L.C. / Tallant, C. / Fedorov, O. / Singleton, D.C. / Rogers, C.M. / Monteiro, O.P. / Bennett, J.M. / Baronio, R. / Muller, S. / Daniels, D.L. / Mendez, J. / Knapp, S. / Brennan, P.E. / Dixon, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zql.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zql.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/4zql ftp://data.pdbj.org/pub/pdb/validation_reports/zq/4zql | HTTPS FTP |
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-Related structure data
Related structure data | 3o33S S: Starting model for refinement |
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Similar structure data |
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21403.547 Da / Num. of mol.: 2 / Fragment: residues 791-972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM24, RNF82, TIF1, TIF1A / Plasmid: pET15 / Production host: Escherichia coli (E. coli) References: UniProt: O15164, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Non-polymers , 6 types, 217 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-4QH / | #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density meas: 397644.281 Mg/m3 / Density % sol: 48.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 2M ammonium sulfate, 2%(v/v) PEG 400 PH range: 7.5-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→27.84 Å / Num. all: 37097 / Num. obs: 37097 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.055 / Rsym value: 0.027 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 3.2 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O33 Resolution: 1.79→27.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.115 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109 / 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: 31.473 Å2
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Refinement step | Cycle: 1 / Resolution: 1.79→27.84 Å
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