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- PDB-6gjk: A degradation product of PD 404182 (P2742) bound to Histone Deace... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gjk | ||||||
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Title | A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase | ||||||
![]() | Histone deacetylase-like amidohydrolase | ||||||
![]() | HYDROLASE / HDAH / HDAC / P2742 / PD 404182 / HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE / HISTONE DEACETYLASE / covalent modification | ||||||
Function / homology | ![]() Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kraemer, A. / Meyer-Almes, F.J. | ||||||
![]() | ![]() Title: Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine. Authors: Muth, M. / Jansch, N. / Kopranovic, A. / Kramer, A. / Wossner, N. / Jung, M. / Kirschhofer, F. / Meyer-Almes, F.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.5 KB | Display | ![]() |
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PDB format | ![]() | 268.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 57.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g1aS S: Starting model for refinement |
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Similar structure data |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40253.480 Da / Num. of mol.: 2 / Mutation: H257P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hdaH, hdaH1 / Plasmid: pET / Production host: ![]() ![]() References: UniProt: Q70I53, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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-Non-polymers , 8 types, 851 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/F0Z.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/F0Z.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MLT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-F0Z / #7: Chemical | #8: Chemical | ChemComp-MLT / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25 / Details: 0.1 M Malate-Imidazole buffer pH 5.25, 4 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→87.77 Å / Num. obs: 152110 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.06 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.47→1.5 Å / CC1/2: 0.791 / Rpim(I) all: 0.409 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5G1A Resolution: 1.47→87.77 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.388 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.193 Å2
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Refinement step | Cycle: 1 / Resolution: 1.47→87.77 Å
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Refine LS restraints |
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