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- PDB-3h61: 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: 3h61 | ||||||
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Title | Catalytic domain of human Serine/Threonine Phosphatase 5 (PP5c) with two Mn2+ atoms originally soaked with norcantharidin (which is present in the structure in the hydrolyzed form) | ||||||
![]() | 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 arachidonate / 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 arachidonate / 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 | ![]() | 286.9 KB | Display | ![]() |
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PDB format | ![]() | 230.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3h60C ![]() 3h62C ![]() 3h63C ![]() 3h64C ![]() 3h66C ![]() 3h67C ![]() 3h68C ![]() 3h69C ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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-MN / #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: 2.36 Å3/Da / Density % sol: 47.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10mM Tris-HC, 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: Jan 25, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→40 Å / Num. all: 115060 / Num. obs: 115060 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 200.1 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.9 / Num. unique all: 15316 / Rsym value: 0.393 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S95 Resolution: 1.45→37.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.229 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.069 / 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: 15.466 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→37.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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