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- PDB-2jds: Structure of cAMP-dependent protein kinase complexed with A-443654 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jds | ||||||
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Title | Structure of cAMP-dependent protein kinase complexed with A-443654 | ||||||
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![]() | TRANSFERASE / CAMP / KINASE / MYRISTATE / LIPOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / PROTEIN KINASE INHIBITOR / ATP-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION | ||||||
Function / homology | ![]() CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / negative regulation of cAMP-dependent protein kinase activity / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A signaling / regulation of G2/M transition of mitotic cell cycle / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Davies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / McHardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. ...Davies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / McHardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. / Jhoti, H. / Barford, D. | ||||||
![]() | ![]() Title: A Structural Comparison of Inhibitor Binding to Pkb, Pka and Pka-Pkb Chimera Authors: Davies, T.G. / Verdonk, M.L. / Graham, B. / Saalau-Bethell, S. / Hamlett, C.C.F. / Mchardy, T. / Collins, I. / Garrett, M.D. / Workman, P. / Woodhead, S.J. / Jhoti, H. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.8 KB | Display | ![]() |
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PDB format | ![]() | 72.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.2 KB | Display | ![]() |
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Full document | ![]() | 793.3 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jdoC ![]() 2jdrC ![]() 2jdtC ![]() 2jdvC ![]() 1ydsS 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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Unit cell |
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Components
#1: Protein | Mass: 40917.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ALPHA-CATALYTIC SUBUNIT / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-L20 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.46 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
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→36 Å / Num. obs: 28286 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 95 |
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Processing
Software | Name: REFMAC / Version: 5.2.0019C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YDS Resolution: 2→36.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.964 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.27 Å
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Refine LS restraints |
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