+Open data
-Basic information
Entry | Database: PDB / ID: 8fbv | ||||||
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Title | Compound 7 bound to procaspase-6 | ||||||
Components | Procaspase-6 | ||||||
Keywords | APOPTOSIS / HYDROLASE/INHIBITOR / inhibitor / procaspase-6 / protease / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / activation of innate immune response / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | ||||||
Authors | Fan, P. / Zhao, Y. / Renslo, A.R. / Arkin, M.R. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6. Authors: Togo, T. / Tram, L. / Denton, L.G. / ElHilali-Pollard, X. / Gu, J. / Jiang, J. / Liu, C. / Zhao, Y. / Zhao, Y. / Zheng, Y. / Zheng, Y. / Yang, J. / Fan, P. / Arkin, M.R. / Harma, H. / Sun, D. ...Authors: Togo, T. / Tram, L. / Denton, L.G. / ElHilali-Pollard, X. / Gu, J. / Jiang, J. / Liu, C. / Zhao, Y. / Zhao, Y. / Zheng, Y. / Zheng, Y. / Yang, J. / Fan, P. / Arkin, M.R. / Harma, H. / Sun, D. / Canan, S.S. / Wheeler, S.E. / Renslo, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fbv.cif.gz | 208.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fbv.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 8fbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fbv_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8fbv_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8fbv_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 8fbv_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/8fbv ftp://data.pdbj.org/pub/pdb/validation_reports/fb/8fbv | HTTPS FTP |
-Related structure data
Related structure data | 8f78C 8f96C 8f97C 8f98C 8f99C 8f9aC 8f9bC 8f9cC 8f9dC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 34121.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P55212, caspase-6 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | 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: 3.5 Å3/Da / Density % sol: 64.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7, 4% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→48.42 Å / Num. obs: 26346 / % possible obs: 60.8 % / Redundancy: 15.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.052 / Rrim(I) all: 0.202 / Χ2: 0.99 / Net I/σ(I): 11.9 / Num. measured all: 402198 |
Reflection shell | Resolution: 2.85→3.01 Å / % possible obs: 4.5 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.683 / Num. measured all: 2895 / Num. unique obs: 284 / CC1/2: 0.95 / Rpim(I) all: 0.223 / Rrim(I) all: 0.719 / Χ2: 0.91 / Net I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→48.42 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.793 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 40.223 Å2
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Refinement step | Cycle: 1 / Resolution: 2.86→48.42 Å
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