[English] 日本語
Yorodumi- PDB-3edr: The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO -
+Open data
-Basic information
Entry | Database: PDB / ID: 3edr | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / CASPASE / PEPTIDE INHIBITOR / APOPTOSIS / THIOL PROTEASE / 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 / cysteine-type peptidase activity / response to UV / striated muscle cell differentiation / protein catabolic process / protein processing / heart development / peptidase activity / neuron apoptotic process / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Agniswamy, J. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3edr.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3edr.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 3edr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3edr ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3edr | HTTPS FTP |
---|
-Related structure data
Related structure data | 3edqC 1f1jS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19564.598 Da / Num. of mol.: 2 / Fragment: P20 subunit (UNP residues 24 to 196) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55210, caspase-7 #2: Protein | Mass: 11352.862 Da / Num. of mol.: 2 / Fragment: P10 subunit (UNP residues 207 to 303) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55210, caspase-7 #3: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 589.594 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The peptide was obtained from EMD chemicals, Inc., NJ. Source: (synth.) Saccharomyces cerevisiae (Baker's yeast) (yeast) References: N-acetyl-L-leucyl-L-alpha-aspartyl-L-alpha-glutamyl-L-seryl-L-aspartic aldehyde, UniProt: P36114*PLUS #4: Water | ChemComp-HOH / | Compound details | THE INHIBITOR IS COVALENTLY | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.62 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.1M Sodium Formate,0.1M Sodium Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2006 |
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: 2.45→50 Å / Num. all: 31796 / Num. obs: 28712 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.52 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.89 / Num. unique all: 1761 / % possible all: 57.3 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1F1J Resolution: 2.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|