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- PDB-3v4o: Human MALT1 (caspase domain) in complex with an irreversible pept... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v4o | ||||||
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Title | Human MALT1 (caspase domain) in complex with an irreversible peptidic inhibitor | ||||||
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![]() | HYDROLASE/INHIBITOR / Caspase / Hydrolase / TRAF6 / BCL10 / Cytosolic / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / response to fungus / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation ...polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / response to fungus / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / small molecule binding / T cell proliferation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / Activation of NF-kappaB in B cells / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / fibrillar center / defense response / FCERI mediated NF-kB activation / ubiquitin-protein transferase activity / : / Downstream TCR signaling / peptidase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / protease binding / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / innate immune response / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Renatus, M. / Wiesmann, C. | ||||||
![]() | ![]() Title: Structural Determinants of MALT1 Protease Activity. Authors: Wiesmann, C. / Leder, L. / Blank, J. / Bernardi, A. / Melkko, S. / Decock, A. / D'Arcy, A. / Villard, F. / Erbel, P. / Hughes, N. / Freuler, F. / Nikolay, R. / Alves, J. / Bornancin, F. / Renatus, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.1 KB | Display | ![]() |
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PDB format | ![]() | 47.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.6 KB | Display | ![]() |
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Full document | ![]() | 434.9 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v4lC ![]() 3v55C ![]() 2pyoS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27709.799 Da / Num. of mol.: 1 / Fragment: UNP residues 329-569 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein/peptide | ![]() References: ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 20% PeG3550, 0.4 Ammonium nitrate, 0.1M Bis-tris propane, VAPOR DIFFUSION, temperature 298K, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2010 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→67.11 Å / Num. obs: 19456 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.2 | |||||||||
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3.6 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2PYO Resolution: 2.1→53.86 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→53.86 Å
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