+Open data
-Basic information
Entry | Database: PDB / ID: 3zns | ||||||
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Title | HDAC7 bound with TFMO inhibitor tmp942 | ||||||
Components | HISTONE DEACETYLASE 7 | ||||||
Keywords | HYDROLASE / ZBG / MBG | ||||||
Function / homology | Function and homology information regulation of mRNA processing / protein deacetylation / histone deacetylase / protein lysine deacetylase activity / negative regulation of non-canonical NF-kappaB signal transduction / cell-cell junction assembly / SUMO transferase activity / histone deacetylase activity / negative regulation of interleukin-2 production / positive regulation of cell migration involved in sprouting angiogenesis ...regulation of mRNA processing / protein deacetylation / histone deacetylase / protein lysine deacetylase activity / negative regulation of non-canonical NF-kappaB signal transduction / cell-cell junction assembly / SUMO transferase activity / histone deacetylase activity / negative regulation of interleukin-2 production / positive regulation of cell migration involved in sprouting angiogenesis / Notch-HLH transcription pathway / protein sumoylation / negative regulation of osteoblast differentiation / vasculogenesis / SUMOylation of DNA damage response and repair proteins / protein kinase C binding / 14-3-3 protein binding / Regulation of PTEN gene transcription / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription corepressor activity / DNA-binding transcription factor binding / chromatin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Lobera, M. / Madauss, K.P. / Pohlhaus, D.T. / Trump, R.P. / Nolan, M.A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 Title: Selective Class Iia Histone Deacetylase Inhibition Via a Non-Chelating Zinc Binding Group Authors: Lobera, M. / Madauss, K.P. / Pohlhaus, D.T. / Wright, Q.G. / Trocha, M. / Schmidt, D.R. / Baloglu, E. / Trump, R.P. / Head, M.S. / Hofmann, G.A. / Murray-Thompson, M. / Schwartz, B. / ...Authors: Lobera, M. / Madauss, K.P. / Pohlhaus, D.T. / Wright, Q.G. / Trocha, M. / Schmidt, D.R. / Baloglu, E. / Trump, R.P. / Head, M.S. / Hofmann, G.A. / Murray-Thompson, M. / Schwartz, B. / Chakravorty, S. / Wu, Z. / Mander, P.K. / Kruidenier, L. / Reid, R.A. / Burkhart, W. / Turunen, B.J. / Rong, J.X. / Wagner, C. / Moyer, M.B. / Wells, C. / Hong, X. / Moore, J.T. / Williams, J.D. / Soler, D. / Ghosh, S. / Nolan, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zns.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zns.ent.gz | 178 KB | Display | PDB format |
PDBx/mmJSON format | 3zns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/3zns ftp://data.pdbj.org/pub/pdb/validation_reports/zn/3zns | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 45518.340 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Details: INHIBITOR / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8WUI4, histone deacetylase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.11 Å3/Da / Density % sol: 41.74 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 10% PEG 3350, 3% ISOPROPANAL, HEPES PH7.5, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97 |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Mar 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 38814 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.6 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→70.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 20.711 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.264 / 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: 26.288 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→70.71 Å
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