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Yorodumi- PDB-1rhj: CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A PRYAZINONE I... -
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-Basic information
Entry | Database: PDB / ID: 1rhj | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A PRYAZINONE INHIBITOR | ||||||
Components | (Caspase-3) x 2 | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEASE / CASPASE-3 / APOPAIN / CPP32 / YAMA / COMPLEX (PROTEASE-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 / cell fate commitment / 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 / 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 / aspartic-type endopeptidase activity / neuron apoptotic process / response to lipopolysaccharide / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Becker, J.W. / Rotonda, J. / Soisson, S.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Reducing the Peptidyl Features of Caspase-3 Inhibitors: A Structural Analysis. Authors: Becker, J.W. / Rotonda, J. / Soisson, S.M. / Aspiotis, R. / Bayly, C. / Francoeur, S. / Gallant, M. / Garcia-Calvo, M. / Giroux, A. / Grimm, E. / Han, Y. / McKay, D. / Nicholson, D.W. / ...Authors: Becker, J.W. / Rotonda, J. / Soisson, S.M. / Aspiotis, R. / Bayly, C. / Francoeur, S. / Gallant, M. / Garcia-Calvo, M. / Giroux, A. / Grimm, E. / Han, Y. / McKay, D. / Nicholson, D.W. / Peterson, E. / Renaud, J. / Roy, S. / Thornberry, N. / Zamboni, R. | ||||||
History |
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Remark 999 | SEQUENCE THE HIS TAGS ON CHAINS B AND D WERE NOT CLEAVED FOR THIS ENTRY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rhj.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rhj.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rhj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rhj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1rhj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1rhj_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 1rhj_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/1rhj ftp://data.pdbj.org/pub/pdb/validation_reports/rh/1rhj | HTTPS FTP |
-Related structure data
Related structure data | 1re1C 1rhkC 1rhmC 1rhqC 1rhrC 1rhuC 1pauS 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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Details | The asymmetric unit contains one biological assembly. |
-Components
#1: Protein | Mass: 16639.902 Da / Num. of mol.: 2 / Fragment: P17 subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Plasmid: pET20b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein | Mass: 12981.756 Da / Num. of mol.: 2 / Fragment: P12 subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #3: Chemical | #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: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 16% PEG-6000, 100 mM citrate, 20 mM L-cysteine, 5 mM glycerol, 3 mM NaN(3), pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→19.9 Å / Num. all: 31682 / Num. obs: 30288 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.36 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.41 % / Rmerge(I) obs: 0.164 / Num. unique all: 2730 / % possible all: 76.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Protein part of 1pau.pdb Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 175071.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.6566 Å2 / ksol: 0.368694 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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