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Open data
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Basic information
Entry | Database: PDB / ID: 7uvn | |||||||||
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Title | Crystal structure of human ClpP protease in complex with TR-57 | |||||||||
![]() | ATP-dependent Clp protease proteolytic subunit, mitochondrial | |||||||||
![]() | HYDROLASE/AGONIST / agonist / protease / degradation / apoptosis / HYDROLASE / HYDROLASE-AGONIST complex | |||||||||
Function / homology | ![]() membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding ...membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / Mitochondrial protein degradation / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mabanglo, M.F. / Houry, W.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Potent ClpP agonists with anticancer properties bind with improved structural complementarity and alter the mitochondrial N-terminome. Authors: Mabanglo, M.F. / Wong, K.S. / Barghash, M.M. / Leung, E. / Chuang, S.H.W. / Ardalan, A. / Majaesic, E.M. / Wong, C.J. / Zhang, S. / Lang, H. / Karanewsky, D.S. / Iwanowicz, A.A. / Graves, L. ...Authors: Mabanglo, M.F. / Wong, K.S. / Barghash, M.M. / Leung, E. / Chuang, S.H.W. / Ardalan, A. / Majaesic, E.M. / Wong, C.J. / Zhang, S. / Lang, H. / Karanewsky, D.S. / Iwanowicz, A.A. / Graves, L.M. / Iwanowicz, E.J. / Gingras, A.C. / Houry, W.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 261.2 KB | Display | ![]() |
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PDB format | ![]() | 209.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 51.4 KB | Display | |
Data in CIF | ![]() | 66.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uvmC ![]() 7uvrC ![]() 7uvuC ![]() 7uw0C ![]() 6bbaS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 24179.875 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-P3O / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, pH 4.6 to 5.2, 5 % PEG 4000 / PH range: 4.6 - 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→50 Å / Num. obs: 35316 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 63.45 Å2 / Rmerge(I) obs: 0.285 / Rpim(I) all: 0.113 / Rrim(I) all: 0.307 / Χ2: 0.857 / Net I/σ(I): 2.6 / Num. measured all: 253214 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BBA Resolution: 3.11→49.25 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.11→49.25 Å
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LS refinement shell |
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