+Open data
-Basic information
Entry | Database: PDB / ID: 8dj3 | ||||||
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Title | Caspase-7 bound to novel allosteric inhibitor | ||||||
Components | Caspase-7 | ||||||
Keywords | APOPTOSIS/APOPTOSIS INHIBITOR / allostery / inhibitor / ternary / APOPTOSIS-APOPTOSIS 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 / heart development / peptidase activity / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Propp, J. / Kalenkiewicz, A. / Kathryn, F.H. / Spies, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemistry / Year: 2023 Title: Allosteric Tuning of Caspase-7: Establishing the Nexus of Structure and Catalytic Power. Authors: Hobbs, K.F. / Propp, J. / Vance, N.R. / Kalenkiewicz, A. / Witkin, K.R. / Ashley Spies, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dj3.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dj3.ent.gz | 121.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/8dj3 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/8dj3 | HTTPS FTP |
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-Related structure data
Related structure data | 8dgzC 1f1jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34566.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7 #2: Chemical | ChemComp-SE1 / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.03 Å3/Da / Density % sol: 59.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.9 M sodium formate, 0.1 M sodium citrate, pH 5.0-5.7 PH range: 5-5.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.8 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jan 12, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→47.89 Å / Num. obs: 11535 / % possible obs: 81 % / Redundancy: 2.2 % / Biso Wilson estimate: 75.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.031 / Rrim(I) all: 0.054 / Net I/σ(I): 15.2 / Num. measured all: 24832 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1f1j Resolution: 3.2→47.89 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 563.12 Å2 / Biso mean: 80.4289 Å2 / Biso min: 27.61 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→47.89 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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