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- PDB-3h69: Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h69 | ||||||
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Title | Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Zn2+ atoms complexed with endothall | ||||||
![]() | Serine/threonine-protein phosphatase 5 | ||||||
![]() | HYDROLASE / metalloenzyme / phosphatase / inhibitors / drug design / Cytoplasm / Iron / Manganese / Metal-binding / Nucleus / Protein phosphatase / TPR repeat | ||||||
Function / homology | ![]() response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity ...response to arachidonic acid / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / response to morphine / protein folding chaperone complex / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / ESR-mediated signaling / response to lead ion / Hsp90 protein binding / tau protein binding / ADP binding / Negative regulation of MAPK pathway / MAPK cascade / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic cell cycle / positive regulation of canonical NF-kappaB signal transduction / intracellular membrane-bounded organelle / DNA-templated transcription / lipid binding / protein-containing complex / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Talluri, E. | ||||||
![]() | ![]() Title: Structural basis of serine/threonine phosphatase inhibition by the archetypal small molecules cantharidin and norcantharidin Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Talluri, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.1 KB | Display | ![]() |
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PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.4 KB | Display | ![]() |
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Full document | ![]() | 484.9 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3h60C ![]() 3h61C ![]() 3h62C ![]() 3h63C ![]() 3h64C ![]() 3h66C ![]() 3h67C ![]() 3h68C ![]() 1s95S C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35950.797 Da / Num. of mol.: 2 / Fragment: Catalytic domain, residues 176-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53041, protein-serine/threonine phosphatase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ENL / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.63 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10mM Tris-HCl, 40% MPD, 20% PEG MME 5000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9834 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 39575 / Num. obs: 39575 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5696 / Rsym value: 0.358 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S95 Resolution: 2.1→38.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.899 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.216 / ESU R Free: 0.191 / 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: 24.974 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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