+Open data
-Basic information
Entry | Database: PDB / ID: 1nx3 | ||||||
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Title | Calpain Domain VI in Complex with the Inhibitor PD150606 | ||||||
Components | Calcium-dependent protease, small subunit | ||||||
Keywords | HYDROLASE / CALCIUM BINDING | ||||||
Function / homology | Function and homology information Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / calcium ion binding / proteolysis / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Todd, B. / Moore, D. / Deivanayagam, C.C.S. / Lin, G.-D. / Chattopadhyay, D. / Maki, M. / Wang, K.K.W. / Narayana, S.V.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nx3.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nx3.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nx3_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 1nx3_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 1nx3_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1nx3_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nx3 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nx3 | HTTPS FTP |
-Related structure data
-Links
-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.: 1 / Fragment: Domain VI Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPNS1 OR CAPN4 / Production host: Escherichia coli (E. coli) / References: UniProt: P04574 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ISA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.22 Å3/Da / Density % sol: 64.76 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop Details: PEG 6000, BME, EDTA, CaCl2, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 6.7 / PH range high: 5.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
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 | Lowest resolution: 100 Å / Num. all: 10626 / Num. obs: 10626 / % possible obs: 99.9 % / Observed criterion σ(F): 2.45 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.8 |
Reflection | *PLUS Highest resolution: 2.45 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→100 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.45→100 Å
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Refinement | *PLUS Rfactor Rwork: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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