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Yorodumi- PDB-8wuz: Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wuz | ||||||
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Title | Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators | ||||||
Components | ATP-dependent Clp protease proteolytic subunit, mitochondrial | ||||||
Keywords | HYDROLASE / Mitochondria / Caseinolytic Protease P / activator / antitumor | ||||||
Function / homology | Function and homology information membrane protein proteolysis / mitochondrial protein catabolic process / endopeptidase Clp / endopeptidase Clp complex / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / 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 / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Jiang, J.-X. / Ding, H. / Chen, M.-R. / Lu, M.-L. / Sun, H.-Y. / Xiao, Y.-B. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators Authors: Jiang, J.-X. / Ding, H. / Chen, M.-R. / Lu, M.-L. / Sun, H.-Y. / Xiao, Y.-B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wuz.cif.gz | 495.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wuz.ent.gz | 412.9 KB | Display | PDB format |
PDBx/mmJSON format | 8wuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wuz_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8wuz_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8wuz_validation.xml.gz | 53.7 KB | Display | |
Data in CIF | 8wuz_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/8wuz ftp://data.pdbj.org/pub/pdb/validation_reports/wu/8wuz | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q16740, endopeptidase Clp #2: Chemical | ChemComp-XFU / Mass: 472.478 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C25H24F4N4O #3: Chemical | ChemComp-BR / Has ligand of interest | N | Has protein modification | N | |
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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: 3.29 Å3/Da / Density % sol: 62.59 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M NaBr, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.75 Å / Num. obs: 83250 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.995 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.9→2.9 Å / Num. unique obs: 6199 / CC1/2: 0.784 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.75 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.1516 Å / Origin y: -37.8464 Å / Origin z: -16.9009 Å
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Refinement TLS group | Selection details: all |