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- PDB-1tl9: High resolution crystal structure of calpain I protease core in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tl9 | ||||||
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Title | High resolution crystal structure of calpain I protease core in complex with leupeptin | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / Covalently-linked inhibitor at the active site cysteine forms a hemithioacetal / hydrolase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() calpain-1 / Degradation of the extracellular matrix / protein catabolic process at postsynapse / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / regulation of catalytic activity / negative regulation of actin filament polymerization / receptor catabolic process / self proteolysis ...calpain-1 / Degradation of the extracellular matrix / protein catabolic process at postsynapse / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / regulation of catalytic activity / negative regulation of actin filament polymerization / receptor catabolic process / self proteolysis / cornified envelope / positive regulation of vascular permeability / response to arsenic-containing substance / negative regulation of non-canonical NF-kappaB signal transduction / response to angiotensin / Neutrophil degranulation / positive regulation of cardiac muscle cell apoptotic process / protein autoprocessing / cytoskeletal protein binding / protein catabolic process / cellular response to hydrogen peroxide / presynapse / peptidase activity / postsynapse / postsynaptic density / lysosome / glutamatergic synapse / calcium ion binding / enzyme binding / mitochondrion / proteolysis / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Moldoveanu, T. / Campbell, R.L. / Cuerrier, D. / Davies, P.L. | ||||||
![]() | ![]() Title: Crystal Structures of Calpain-E64 and -Leupeptin Inhibitor Complexes Reveal Mobile Loops Gating the Active Site Authors: Moldoveanu, T. / Campbell, R.L. / Cuerrier, D. / Davies, P.L. #1: ![]() Title: A calcium switch aligns the active site of calpain Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Elce, J.S. / Jia, Z. / Davies, P.L. #2: ![]() Title: calpain silencing by a reversible intrinsic mechanism Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Jia, Z. / Davies, P.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 64 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 38804.551 Da / Num. of mol.: 1 / Fragment: residues 27-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE LEUPEPTIN IS COVALENTLY | Sequence details | THERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ...THERE IS A DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | pH: 6 Details: sodium chloride, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 31962 / % possible obs: 95 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.069 / Rsym value: 0.072 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 14.9 / Num. measured obs: 3221 / Rsym value: 0.152 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KXRB Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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