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Yorodumi- PDB-1f1j: CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f1j | ||||||
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Title | CRYSTAL STRUCTURE OF CASPASE-7 IN COMPLEX WITH ACETYL-ASP-GLU-VAL-ASP-CHO | ||||||
Components |
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Keywords | APOPTOSIS / HYDROLASE/HYDROLASE INHIBITOR / caspase-7 / cysteine protease / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / 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 / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å | ||||||
Authors | Wei, Y. / Charifson, P.S. | ||||||
Citation | Journal: Chem.Biol. / Year: 2000 Title: The structures of caspases-1, -3, -7 and -8 reveal the basis for substrate and inhibitor selectivity. Authors: Wei, Y. / Fox, T. / Chambers, S.P. / Sintchak, J. / Coll, J.T. / Golec, J.M. / Swenson, L. / Wilson, K.P. / Charifson, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f1j.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f1j.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 1f1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f1j_validation.pdf.gz | 403.1 KB | Display | wwPDB validaton report |
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Full document | 1f1j_full_validation.pdf.gz | 408.1 KB | Display | |
Data in XML | 1f1j_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1f1j_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/1f1j ftp://data.pdbj.org/pub/pdb/validation_reports/f1/1f1j | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 34550.031 Da / Num. of mol.: 2 / Fragment: P20/P10 CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P55210, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein/peptide | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS186A AND ATOM C OF ASA705C, AND SAME BOND BETWEEN ...THERE IS A COVALENT BOND BETWEEN ATOM SG OF CYS186A AND ATOM C OF ASA705C, AND SAME BOND BETWEEN ATOM SG OF CYS486B AND ATOM C OF ASA805D, FORMING THIOHEMIAC | |
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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: 2.98 Å3/Da / Density % sol: 58.73 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 4000, 0.1 M Na-citrate, 0.2 M ammonium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 128 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Sep 20, 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: 2.35→20 Å / Num. all: 35568 / Num. obs: 34359 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.35→2.42 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / % possible all: 92.3 |
Reflection | *PLUS Num. measured all: 139781 |
-Processing
Software |
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Refinement | Resolution: 2.35→7.5 Å / σ(F): 2.5 / σ(I): 1.6 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.35→7.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7.5 Å / σ(F): 2.5 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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