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- PDB-3dej: Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-tri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dej | ||||||
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Title | Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors | ||||||
![]() | Caspase-3 | ||||||
![]() | Hydrolase / Apoptosis / Caspase-3 / Isoquinoline-1 / 3 / 4-trione derivatives / Inactivation / protein-inhibitor complex / Cytoplasm / Phosphoprotein / Polymorphism / Protease / S-nitrosylation / Thiol protease / Zymogen | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, J. / Du, J. / Li, J. / Ding, J. | ||||||
![]() | ![]() Title: Isoquinoline-1,3,4-trione Derivatives Inactivate Caspase-3 by Generation of Reactive Oxygen Species Authors: Du, J.-Q. / Wu, J. / Zhang, H.-J. / Zhang, Y.-H. / Qiu, B.-Y. / Wu, F. / Chen, Y.-H. / Li, J.-Y. / Nan, F.-J. / Ding, J.-P. / Li, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 370.6 KB | Display | ![]() |
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PDB format | ![]() | 302.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 911.2 KB | Display | ![]() |
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Full document | ![]() | 930.7 KB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 50.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dehC ![]() 3deiC ![]() 3dekC ![]() 1gfwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28566.500 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-RXC / ( | #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR WAS SYNTHESIZE | Sequence details | 190TH RESIDUE IN ALL CHAINS IS ASP AND IS A NATURAL VARIANT FOR CASP3_HUMAN. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.75 % / Mosaicity: 0.494 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 4-6% polyethylene glycol 6000, 0.1M HEPES pH 7.6, 20mM L-cysteine, 5% glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 23, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 35800 / % possible obs: 99.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.121 / Χ2: 1.085 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.482 / Num. unique all: 3338 / Χ2: 0.385 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GFW Resolution: 2.6→46.45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.196 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.071 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→46.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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