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Yorodumi- PDB-7uso: Crystal Structure of Caspase-3 with Peptide Inhibitor AcITVKD-CHO -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uso | ||||||
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Title | Crystal Structure of Caspase-3 with Peptide Inhibitor AcITVKD-CHO | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Complex / Peptide Inhibitor / Covalent inhibitor / APOPTOSIS / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / response to amino acid / cell fate commitment / regulation of macroautophagy / response to tumor necrosis factor / Pyroptosis / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / enzyme activator activity / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Fuller, J.L. / Finzel, B.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch Pharm / Year: 2022 Title: Characterization of caspase-2 inhibitors based on specific sites of caspase-2-mediated proteolysis. Authors: Bresinsky, M. / Strasser, J.M. / Hubmann, A. / Vallaster, B. / McCue, W.M. / Fuller, J. / Singh, G. / Nelson, K.M. / Cuellar, M.E. / Finzel, B.C. / Ashe, K.H. / Walters, M.A. / Pockes, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uso.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uso.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 7uso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uso_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 7uso_full_validation.pdf.gz | 471.3 KB | Display | |
Data in XML | 7uso_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 7uso_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/7uso ftp://data.pdbj.org/pub/pdb/validation_reports/us/7uso | HTTPS FTP |
-Related structure data
Related structure data | 7rnaC 7rngC 7uspC 7usqC 7rnfS S: Starting model for refinement 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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Unit cell |
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-Components
#1: Protein | Mass: 16639.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3 #2: Protein | Mass: 11910.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574 #3: Protein/peptide | Mass: 601.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: 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: 2.51 Å3/Da / Density % sol: 51.06 % / Description: plate crystals grow within 48 hours |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 15% PEG 6000, 5% Glycerol, 100mM Sodium Citrate (pH 5.3), 10mM DTT, 3mM NaN3 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2021 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.31 Å / Num. obs: 23912 / % possible obs: 98.11 % / Redundancy: 1.9 % / Biso Wilson estimate: 35.78 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.04781 / Rpim(I) all: 0.04781 / Rrim(I) all: 0.06761 / Net I/σ(I): 8.34 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 2 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 2395 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.201 / Rrim(I) all: 0.2843 / % possible all: 99.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7rnf Resolution: 2.3→36.31 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.45 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.61 Å2 / Biso mean: 39.2733 Å2 / Biso min: 22.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→36.31 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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