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Open data
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Basic information
Entry | Database: PDB / ID: 1nx0 | ||||||
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Title | Structure of Calpain Domain 6 in Complex with Calpastatin DIC | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / CALCIUM BINDING / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() calcium-dependent cysteine-type endopeptidase inhibitor activity / Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / protein catabolic process / calcium ion binding / proteolysis / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Todd, B. / Moore, D. / Deivanayagam, C.C.S. / Lin, G.-D. / Chattopadhyay, D. / Maki, M. / Wang, K.K.W. / Narayana, S.V.L. | ||||||
![]() | ![]() Title: A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor. Authors: Todd, B. / Moore, D. / Deivanayagam, C.C.S. / Lin, G.-D. / Chattopadhyay, D. / Maki, M. / Wang, K.K.W. / Narayana, S.V.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 | ![]() | 91.4 KB | Display | ![]() |
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PDB format | ![]() | 68.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 391.3 KB | Display | ![]() |
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Full document | ![]() | 403.7 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 19883.477 Da / Num. of mol.: 2 / Fragment: Domain VI Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1241.261 Da / Num. of mol.: 2 / Fragment: DIC, residues 230-241 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | | Mass: 473.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE Peptide WAS CHEMICALLY SYNTHESIZED. #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 6000, BME, EDTA, CaCl2, NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. all: 18854 / Num. obs: 18854 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5 |
Reflection | *PLUS Highest resolution: 2.3 Å / Rmerge(I) obs: 0.06 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.3→100 Å
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Refinement | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.264 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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