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- PDB-3edr: The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO -
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Open data
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Basic information
Entry | Database: PDB / ID: 3edr | ||||||
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Title | The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / CASPASE / PEPTIDE INHIBITOR / APOPTOSIS / THIOL PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 / mitochondrial outer membrane / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Agniswamy, J. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.9 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.2 KB | Display | ![]() |
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Full document | ![]() | 477 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3edqC ![]() 1f1jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #3: Protein/peptide | ![]() Details: The peptide was obtained from EMD chemicals, Inc., NJ. Source: (synth.) ![]() ![]() 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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.62 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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