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Open data
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Basic information
Entry | Database: PDB / ID: 6bfo | ||||||
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Title | Caspase-3 Mutant- T245D | ||||||
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![]() | apoptosis/inhibitor / allosteric regulation / apoptosis / biophysics / caspase / computational biology / X-ray crystallography / fluorescence / molecular dynamics / protein evolution / apoptosis-inhibitor complex | ||||||
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 / cellular response to staurosporine / cyclin-dependent protein serine/threonine kinase inhibitor activity / 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 / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / execution phase of apoptosis / 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 / response to amino acid / Caspase-mediated cleavage of cytoskeletal proteins / 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 / regulation of protein stability / protein catabolic process / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / protein-containing complex binding / apoptotic process / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thomas, M.E. / Grinshpon, R. / Swartz, P.D. / Clark, A.C. | ||||||
![]() | ![]() Title: Modifications to a common phosphorylation network provide individualized control in caspases. Authors: Thomas, M.E. / Grinshpon, R. / Swartz, P. / Clark, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 55.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bdvC ![]() 6bfjC ![]() 6bfkC ![]() 6bflC ![]() 6bg0C ![]() 6bg1C ![]() 6bg4C ![]() 6bgkC ![]() 6bgqC ![]() 6bgrC ![]() 6bgsC ![]() 6bh9C ![]() 6bhaC C: citing same article ( |
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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 on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 19759.344 Da / Num. of mol.: 1 / Mutation: T245D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 12062.733 Da / Num. of mol.: 1 / Mutation: T245D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules D
#3: Protein/peptide | |
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-Non-polymers , 3 types, 298 molecules ![](data/chem/img/NA.gif)
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#4: Chemical | ChemComp-NA / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM ...Details: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. obs: 41341 / % possible obs: 99.9 % / Redundancy: 6.4 % / Net I/σ(I): 26.7 |
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Processing
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Refinement | Resolution: 1.54→35.592 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.78 Details: Authors indicate that is not possible to define the covalent bond between the cysteine sulfur atom and the carbon atom of the inhibitor in Phenix
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→35.592 Å
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Refine LS restraints |
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LS refinement shell |
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