+Open data
-Basic information
Entry | Database: PDB / ID: 3edq | ||||||
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Title | Crystal structure of Caspase-3 with inhibitor AC-LDESD-CHO | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ENZYME CATALYSIS / CYSTEINE PROTEASE / APOPTOSIS / S-NITROSYLATION / THIOL PROTEASE / 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 / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / 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 / pyroptotic inflammatory response / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / regulation of macroautophagy / response to amino acid / cell fate commitment / Pyroptosis / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / response to nicotine / apoptotic signaling pathway / hippocampus development / sensory perception of sound / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / protein processing / neuron differentiation / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / response to hypoxia / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Fu, G. | ||||||
Citation | Journal: Apoptosis / Year: 2008 Title: Structural basis for executioner caspase recognition of P5 position in substrates. Authors: Fu, G. / Chumanevich, A.A. / Agniswamy, J. / Fang, B. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3edq.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3edq.ent.gz | 175.1 KB | Display | PDB format |
PDBx/mmJSON format | 3edq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3edq ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3edq | HTTPS FTP |
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-Related structure data
Related structure data | 3edrC 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: 16639.902 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 29-175 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Plasmid: PET23B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P42574, caspase-3 #2: Protein | Mass: 12739.485 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 176-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Plasmid: PET23B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P42574, caspase-3 #3: Protein/peptide | Mass: 587.578 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Ac-LDESD-CHO, obtained from EMD Chemicals, Inc., NJ. #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: 2.42 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 MM SODIUM CITRATE, 5% GLYCEROL, 10 MM DITHIOTHREITOL AND 14-18% PEG6000, PH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2007 |
Radiation | Monochromator: SI 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→50 Å / Num. all: 72895 / Num. obs: 72601 / % possible obs: 90.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.61→1.67 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.4 / % possible all: 63.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H65 Resolution: 1.61→10 Å / Num. parameters: 37467 / Num. restraintsaints: 46438 / Cross valid method: FREE R / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4154 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→10 Å
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Refine LS restraints |
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