+Open data
-Basic information
Entry | Database: PDB / ID: 8ylb | ||||||
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Title | Cocrystal structures of agonists compound 1 with HsClpP | ||||||
Components | ATP-dependent Clp protease proteolytic subunit, mitochondrial | ||||||
Keywords | HYDROLASE / Homo sapiens Casein lysing protease P (HsClpP) acute myeloid leukemia (AML) agonists | ||||||
Function / homology | Function and homology information membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix ...membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / 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: 2.15 Å | ||||||
Authors | Zhao, N. / Zhu, Y. / Bao, R. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Rational Design of a Novel Class of Human ClpP Agonists through a Ring-Opening Strategy with Enhanced Antileukemia Activity. Authors: Xiang, X. / Dai, Z. / Luo, B. / Zhao, N. / Liu, S. / Sui, J. / Huang, J. / Zhou, Y. / Gu, J. / Zhang, J. / Yang, T. / Bao, R. / Luo, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ylb.cif.gz | 484.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ylb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8ylb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/8ylb ftp://data.pdbj.org/pub/pdb/validation_reports/yl/8ylb | HTTPS FTP |
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-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: 24092.797 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q16740, endopeptidase Clp #2: Chemical | ChemComp-A1LZA / Mass: 386.489 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: C24H26N4O / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.6 M Li2SO4 and 0.1 M Tris, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→19.88 Å / Num. obs: 153963 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.964 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.103 / Rrim(I) all: 0.269 / Χ2: 1.06 / Net I/σ(I): 5 / Num. measured all: 1061470 |
Reflection shell | Resolution: 2.15→2.19 Å / % possible obs: 99.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.823 / Num. measured all: 54255 / Num. unique obs: 7595 / CC1/2: 0.871 / Rpim(I) all: 0.328 / Rrim(I) all: 0.886 / Χ2: 1.13 / Net I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.88 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.66 / 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: 2.15→19.88 Å
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Refine LS restraints |
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LS refinement shell |
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