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Yorodumi- PDB-4zvz: Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicycl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zvz | ||||||
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Title | Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid | ||||||
Components | Serine/threonine-protein phosphatase 5 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Protein phosphatase 5 / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information 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 / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wierzbicki, A. / Honkanen, R.E. | ||||||
Citation | Journal: Biochem. Pharmacol. / Year: 2016 Title: Crystal structures and mutagenesis of PPP-family ser/thr protein phosphatases elucidate the selectivity of cantharidin and novel norcantharidin-based inhibitors of PP5C. Authors: Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wood, E. / D'Arcy, B. / Zivanov, C. / Abney, K. / Musiyenko, A. / Rusin, S.F. / Kettenbach, A. / Yet, L. / Schroeder, C.E. / Golden, J.E. / ...Authors: Chattopadhyay, D. / Swingle, M.R. / Salter, E.A. / Wood, E. / D'Arcy, B. / Zivanov, C. / Abney, K. / Musiyenko, A. / Rusin, S.F. / Kettenbach, A. / Yet, L. / Schroeder, C.E. / Golden, J.E. / Dunham, W.H. / Gingras, A.C. / Banerjee, S. / Forbes, D. / Wierzbicki, A. / Honkanen, R.E. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Structural basis for the catalytic activity of human serine/threonine protein phosphatase-5. Authors: Swingle, M.R. / Honkanen, R.E. / Ciszak, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zvz.cif.gz | 516.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zvz.ent.gz | 428.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zvz ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zvz | HTTPS FTP |
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-Related structure data
Related structure data | 4zx2C 1s95S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37887.020 Da / Num. of mol.: 4 / Fragment: UNP residues 169-499 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP5C, PPP5 / Plasmid: pMal2cE / Production host: Escherichia coli (E. coli) References: UniProt: P53041, protein-serine/threonine phosphatase |
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-Non-polymers , 5 types, 298 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-4TF / ( #4: Chemical | ChemComp-NA / | #5: Chemical | #6: 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: 1.97 Å3/Da / Density % sol: 37.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% MPD, 6% PEG, 10 mM Tris, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→91.03 Å / Num. obs: 76635 / % possible obs: 97.9 % / Redundancy: 2.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.074 / Net I/σ(I): 11.7 / Num. measured all: 183306 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.4 % / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1s95 Resolution: 2→91.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.914 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 33.285 Å2
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Refinement step | Cycle: LAST / Resolution: 2→91.03 Å
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Refine LS restraints |
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