[English] 日本語
Yorodumi- PDB-1gfw: THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gfw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR. | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / CASPASE INHIBITOR / CASPASE-3 / APOPAIN / ISTIN SULFONAMIDE | |||||||||
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 / Apoptotic cleavage of cell adhesion proteins / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / 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 / Resolution: 2.8 Å | |||||||||
Authors | Concha, N.O. / Janson, C.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Potent and selective nonpeptide inhibitors of caspases 3 and 7 inhibit apoptosis and maintain cell functionality. Authors: Lee, D. / Long, S.A. / Adams, J.L. / Chan, G. / Vaidya, K.S. / Francis, T.A. / Kikly, K. / Winkler, J.D. / Sung, C.M. / Debouck, C. / Richardson, S. / Levy, M.A. / DeWolf Jr., W.E. / Keller, ...Authors: Lee, D. / Long, S.A. / Adams, J.L. / Chan, G. / Vaidya, K.S. / Francis, T.A. / Kikly, K. / Winkler, J.D. / Sung, C.M. / Debouck, C. / Richardson, S. / Levy, M.A. / DeWolf Jr., W.E. / Keller, P.M. / Tomaszek, T. / Head, M.S. / Ryan, M.D. / Haltiwanger, R.C. / Liang, P.H. / Janson, C.A. / McDevitt, P.J. / Johanson, K. / Concha, N.O. / Chan, W. / Abdel-Meguid, S.S. / Badger, A.M. / Lark, M.W. / Nadeau, D.P. / Suva, L.J. / Gowen, M. / Nuttall, M.E. #1: Journal: J.Biol.Chem. / Year: 1994 Title: CPP32, a novel human apoptotic protein with homology to Caenorhabditis elegans cell death protein ced-3 and mammalian interleukin-1-b-converting enzyme Authors: Fernandes-Alnemri, T. / Litwack, G. / Alnemri, E.S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gfw.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gfw.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gf/1gfw ftp://data.pdbj.org/pub/pdb/validation_reports/gf/1gfw | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16639.902 Da / Num. of mol.: 1 Fragment: ACTIVATED MATURE CASPASE-3 (P20) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 29-175) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HUMAN T-LYMPHOCYTE CELL LINE JURKAT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42574 |
---|---|
#2: Protein | Mass: 11423.142 Da / Num. of mol.: 1 Fragment: ACTIVATED MATURE CASPASE-3 (P10) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 181-277) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42574 |
#3: Chemical | ChemComp-MSI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M ...Details: 4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 7014 / Num. obs: 6775 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.267 / Num. unique all: 692 / % possible all: 82.4 |
Reflection | *PLUS Num. measured all: 113422 |
Reflection shell | *PLUS % possible obs: 82.4 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.8→40 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1413969.37 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: see Engh & Huber (1991) Acta Cryst A 47, 392-400. Details: Data collection proceeded in the presence of "ice-rings"
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 0.363132 Å2 / ksol: 33.276 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|