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Open data
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Basic information
Entry | Database: PDB / ID: 5vlo | ||||||
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Title | The structure of human CamKII with bound inhibitor | ||||||
![]() | Calcium/calmodulin-dependent protein kinase type II subunit delta | ||||||
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Function / homology | ![]() regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / calcium- and calmodulin-dependent protein kinase complex / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Somoza, J.R. / Villasenor, A.G. | ||||||
![]() | ![]() Title: Inhibitors of CamKII Authors: Somoza, T.J. / Villasenor, A.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.4 KB | Display | ![]() |
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PDB format | ![]() | 107.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34459.574 Da / Num. of mol.: 2 / Fragment: UNP residues 3-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q13557, ![]() #2: Chemical | #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. ...Details: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2016 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→50 Å / Num. obs: 38959 / % possible obs: 98.5 % / Redundancy: 13 % / Biso Wilson estimate: 34.660655594 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.05→2.17 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 5733 / CC1/2: 0.742 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.0908881426 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→47.38 Å
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Refine LS restraints |
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LS refinement shell |
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