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- PDB-6ypg: Crystal Structure of CK2alpha with Compound 2 bound to second cry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ypg | ||||||
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Title | Crystal Structure of CK2alpha with Compound 2 bound to second crystal form | ||||||
![]() | Casein kinase II subunit alpha![]() | ||||||
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Function / homology | ![]() regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Brear, P. / Hyvonen, M. | ||||||
![]() | ![]() Title: Proposed Allosteric Inhibitors Bind to the ATP Site of CK2 alpha. Authors: Brear, P. / Ball, D. / Stott, K. / D'Arcy, S. / Hyvonen, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.1 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yphC ![]() 6ypjC ![]() 6ypkC ![]() 6ypnC ![]() 5cu6S S: Starting model for refinement C: citing same article ( |
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Similar 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: 39031.391 Da / Num. of mol.: 1 / Mutation: R21S, K74A, K75A, K76A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P68400, ![]() |
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#2: Chemical | ChemComp-N5Q / |
#3: Chemical | ChemComp-ACT / ![]() |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 112.5mM Mes, 35% glycerol ethoxylate, 180 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.51→59.56 Å / Num. obs: 47579 / % possible obs: 97.6 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 15.5 / Num. measured all: 316989 / Scaling rejects: 590 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5CU6 Resolution: 1.51→59.56 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 109.24 Å2 / Biso mean: 28.336 Å2 / Biso min: 7.19 Å2
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Refinement step | Cycle: final / Resolution: 1.51→59.56 Å
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LS refinement shell | Resolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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