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Open data
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Basic information
Entry | Database: PDB / ID: 7wh5 | ||||||||||||
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Title | Crystal structure of human ClpP in complex with ZG180 | ||||||||||||
![]() | ATP-dependent Clp protease proteolytic subunit, mitochondrial | ||||||||||||
![]() | HYDROLASE / protease | ||||||||||||
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 / proteolysis involved in protein catabolic process / Mitochondrial protein degradation / ATPase binding / peptidase activity ...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 / proteolysis involved in protein catabolic process / Mitochondrial protein degradation / ATPase binding / peptidase activity / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wei, B.Y. / Gan, J.H. / Yang, C.-G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP. Authors: Wei, B. / Zhang, T. / Wang, P. / Pan, Y. / Li, J. / Chen, W. / Zhang, M. / Ji, Q. / Wu, W. / Lan, L. / Gan, J. / Yang, C.G. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 474.9 KB | Display | ![]() |
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PDB format | ![]() | 387.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7wgsC ![]() 7widC ![]() 7xbzC ![]() 1tg6S 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
#1: Protein | Mass: 24189.912 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-9DF / ( #3: Chemical | ChemComp-MG / | #4: 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: 2.1 Å3/Da / Density % sol: 41.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3350 PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2021 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.13→54.38 Å / Num. obs: 156976 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 6 | ||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1TG6 Resolution: 2.13→54.33 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.868 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 158.65 Å2 / Biso mean: 51.405 Å2 / Biso min: 23.43 Å2
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Refinement step | Cycle: final / Resolution: 2.13→54.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.182 Å / Rfactor Rfree error: 0
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