+Open data
-Basic information
Entry | Database: PDB / ID: 7rna | ||||||||||||
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Title | Crystal structure of caspase-3 with inhibitor Ac-ITV(Dab)D-CHO | ||||||||||||
Components |
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Keywords | HYDROLASE / Hydrolase/Hydrolase Inhibitor | ||||||||||||
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 / 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 | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | McCue, W. / 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 | 7rna.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rna.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/7rna ftp://data.pdbj.org/pub/pdb/validation_reports/rn/7rna | HTTPS FTP |
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-Related structure data
Related structure data | 7rngC 7usoC 7uspC 7usqC 2h65S 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: 16067.288 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 BL21(DE3) (bacteria) / References: UniProt: P42574 #2: Protein | Mass: 11257.953 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 BL21(DE3) (bacteria) / References: UniProt: P42574 #3: Protein/peptide | Mass: 556.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 51.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16% PEG 6000, 5% glycerol, 100 mM sodium citrate pH 6.5, and 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→83.21 Å / Num. obs: 41055 / % possible obs: 95.6 % / Redundancy: 2.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.037 / Rrim(I) all: 0.06 / Net I/σ(I): 10.8 / Num. measured all: 88180 / Scaling rejects: 1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.505 / Num. unique obs: 6118 / CC1/2: 0.765 / Rpim(I) all: 0.391 / Rrim(I) all: 0.642 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H65 Resolution: 1.9→43.2 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3875 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 34.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.2 Å
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Refine LS restraints |
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LS refinement shell |
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