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- PDB-2gfc: cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gfc | ||||||
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Title | cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24 | ||||||
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![]() | TRANSFERASE / binary complex / peptide inhibitor | ||||||
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 / AMP-activated protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / molecular function inhibitor activity / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / molecular adaptor activity / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bonn, S. / Herrero, S. / Breitenlechner, C.B. / Engh, R.A. / Gassel, M. / Bossemeyer, D. | ||||||
![]() | ![]() Title: Structural Analysis of Protein Kinase A Mutants with Rho-kinase Inhibitor Specificity. Authors: Bonn, S. / Herrero, S. / Breitenlechner, C.B. / Erlbruch, A. / Lehmann, W. / Engh, R.A. / Gassel, M. / Bossemeyer, 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 | ![]() | 92.9 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2gnfC ![]() 2gngC ![]() 2gnhC ![]() 2gniC ![]() 2gnjC ![]() 2gnlC 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: 40706.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: Inhibitory Fragment (Residues: 5 to 24) / Source method: obtained synthetically / Details: Peptide Synthesis / References: UniProt: P61926 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15 % Methanol, 75 mM LiCl, 30 mM MesBisTris, 1 mM DTT, 0.2 mM EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00076 Å / Relative weight: 1 |
Reflection | Resolution: 1.642→55.048 Å / Num. all: 54383 / Num. obs: 54188 / % possible obs: 99.77 % / Observed criterion σ(F): 514.1 / Observed criterion σ(I): 4.9 |
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Processing
Software | Name: REFMAC / Version: 5.1.24 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: AN UNPUBLISHED STRUCTURE OF THE BINARY COMPLEX OF BOVINE PKA C ALPHA ENZYME WITH PKI(5-24) Resolution: 1.87→55.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.106 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.139 / ESU R Free: 0.138 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.139 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→55.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.919 Å / Total num. of bins used: 20 /
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