+Open data
-Basic information
Entry | Database: PDB / ID: 7rne | ||||||||||||
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Title | Crystal structure of caspase-3 with inhibitor Ac-YKPVD-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 / 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) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||||||||
Authors | McCue, W. / Finzel, B.C. | ||||||||||||
Funding support | United States, 1items
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Citation | Journal: Acs Pharmacol Transl Sci / Year: 2022 Title: Structure-Based Design and Biological Evaluation of Novel Caspase-2 Inhibitors Based on the Peptide AcVDVAD-CHO and the Caspase-2-Mediated Tau Cleavage Sequence YKPVD314. Authors: Bresinsky, M. / Strasser, J.M. / Vallaster, B. / Liu, P. / McCue, W.M. / Fuller, J. / Hubmann, A. / Singh, G. / Nelson, K.M. / Cuellar, M.E. / Wilmot, C.M. / Finzel, B.C. / Ashe, K.H. / ...Authors: Bresinsky, M. / Strasser, J.M. / Vallaster, B. / Liu, P. / McCue, W.M. / Fuller, J. / Hubmann, A. / Singh, G. / Nelson, K.M. / Cuellar, M.E. / Wilmot, C.M. / 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 | 7rne.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rne.ent.gz | 80.2 KB | Display | PDB format |
PDBx/mmJSON format | 7rne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rne_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 7rne_full_validation.pdf.gz | 451.5 KB | Display | |
Data in XML | 7rne_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 7rne_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/7rne ftp://data.pdbj.org/pub/pdb/validation_reports/rn/7rne | HTTPS FTP |
-Related structure data
Related structure data | 7rn7C 7rn8C 7rn9C 7rnbC 7rndC 7rnfC 7seoC 2h65S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 631.740 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Water | ChemComp-HOH / | |
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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: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15% PEG 6000, 5% glycerol (v:v), 100 mM sodium citrate pH 5.3, 10 mM DTT, and 30 mM NaN3 |
-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: Mar 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→63.38 Å / Num. obs: 15257 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.054 / Rrim(I) all: 0.145 / Net I/σ(I): 10.4 / Num. measured all: 108478 |
Reflection shell | Resolution: 2.73→2.88 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.584 / Num. unique obs: 2174 / CC1/2: 0.951 / Rpim(I) all: 0.225 / Rrim(I) all: 0.627 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H65 Resolution: 2.73→63.38 Å / SU ML: 0.346 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.5592 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: 42.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→63.38 Å
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Refine LS restraints |
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LS refinement shell |
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