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Open data
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Basic information
Entry | Database: PDB / ID: 2xzd | ||||||
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Title | Caspase-3 in Complex with an Inhibitory DARPin-3.4 | ||||||
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![]() | HYDROLASE/PROTEIN BINDING / HYDROLASE-PROTEIN BINDING COMPLEX / DE NOVO PROTEIN / APOPTOSIS / ANKYRIN REPEAT PROTEIN / RIBOSOME DISPLAY | ||||||
Function / homology | ![]() 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 / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / 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 / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / B cell homeostasis / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / response to amino acid / cell fate commitment / regulation of macroautophagy / response to tumor necrosis factor / Pyroptosis / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / enzyme activator activity / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barandun, J. / Schroeder, T. / Mittl, P. / Grutter, M.G. | ||||||
![]() | ![]() Title: Specific Inhibition of Caspase-3 by a Competitive Darpin: Molecular Mimicry between Native and Designed Inhibitors. Authors: Schroeder, T. / Barandun, J. / Flutsch, A. / Briand, C. / Mittl, P. / Grutter, M.G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.2 KB | Display | ![]() |
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PDB format | ![]() | 245.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.3 KB | Display | ![]() |
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Full document | ![]() | 506.5 KB | Display | |
Data in XML | ![]() | 30.7 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y0bC ![]() 2dkoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 6 molecules ACBDGH
#1: Protein | Mass: 16874.174 Da / Num. of mol.: 2 / Fragment: P17 SUBUNIT, RESIDUES 29-175 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 13832.739 Da / Num. of mol.: 2 / Fragment: P12 SUBUNIT, RESIDUES 176-277 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 14740.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: IN-VITRO EVOLVED SEQUENCE / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ![]() ![]() |
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-Non-polymers , 3 types, 321 molecules ![](data/chem/img/MRD.gif)
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#4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | CHAIN A AND C, ASP 28 TO SER MUTATIONS FROM CLONING STRATEGY. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.3 Details: 100 MM HEPES, PH 7.3 (RT), 40 % 2-METHYL-2,4-PENTANEDIOL. |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2010 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49 Å / Num. obs: 63172 / % possible obs: 99.3 % / Observed criterion σ(I): 1.92 / Redundancy: 3.9 % / Biso Wilson estimate: 35.29 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.59 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.92 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DKO Resolution: 2.1→49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 10.66 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→49 Å
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