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- PDB-7lcb: C1B domain of Protein kinase C in complex with prostratin and pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lcb | ||||||
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Title | C1B domain of Protein kinase C in complex with prostratin and phosphatidylcholine | ||||||
![]() | Protein kinase C delta type | ||||||
![]() | LIPID BINDING PROTEIN / C1 / lipid-binding / diacylglycerol-binding / Zn2+ finger | ||||||
Function / homology | ![]() protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / intracellular signal transduction / cell cycle / phosphorylation / apoptotic process / perinuclear region of cytoplasm / ATP binding / nucleus / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Katti, S.S. / Krieger, I.V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural anatomy of Protein Kinase C C1 domain interactions with diacylglycerol and other agonists. Authors: Katti, S.S. / Krieger, I.V. / Ann, J. / Lee, J. / Sacchettini, J.C. / Igumenova, T.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.7 KB | Display | ![]() |
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PDB format | ![]() | 15.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kndC ![]() 7knjC ![]() 7ko6C ![]() 7l92C ![]() 7leoC ![]() 7lf3C ![]() 1ptqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 6097.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-XYV / | #4: Chemical | ChemComp-XP5 / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Screen condition: 0.2 M Ammonium acetate 0.1 M Sodium Phosphate 30% Isopropanol pH 6.8; Drop condition: Protein: 2 mM in MES pH 6.5, 150 mM KCl; Phosphatidylcholine: 20 mM; Prostratin: 2.5 mM |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Sep 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.6 Å / Num. obs: 5115 / % possible obs: 89.1 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.0558 / Net I/σ(I): 15.48 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.2636 / Mean I/σ(I) obs: 3 / Num. unique obs: 441 / % possible all: 48.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ptq Resolution: 1.7→28.75 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 52.92 Å2 / Biso mean: 17.4806 Å2 / Biso min: 4.92 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→28.75 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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