[English] 日本語
Yorodumi- PDB-5vib: Crystal structure of Protein Kinase A in complex with the PKI pep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vib | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Protein Kinase A in complex with the PKI peptide and Aminobenzothiazole based inhibitors | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / Kinase | ||||||
Function / homology | Function and homology information 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 / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / 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 / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 Å | ||||||
Authors | Judge, R.A. | ||||||
Citation | Journal: Chembiochem / Year: 2018 Title: Design of Aminobenzothiazole Inhibitors of Rho Kinases 1 and 2 by Using Protein Kinase A as a Structure Surrogate. Authors: Judge, R.A. / Vasudevan, A. / Scott, V.E. / Simler, G.H. / Pratt, S.D. / Namovic, M.T. / Putman, C.B. / Aguirre, A. / Stoll, V.S. / Mamo, M. / Swann, S.I. / Cassar, S.C. / Faltynek, C.R. / ...Authors: Judge, R.A. / Vasudevan, A. / Scott, V.E. / Simler, G.H. / Pratt, S.D. / Namovic, M.T. / Putman, C.B. / Aguirre, A. / Stoll, V.S. / Mamo, M. / Swann, S.I. / Cassar, S.C. / Faltynek, C.R. / Kage, K.L. / Boyce-Rustay, J.M. / Hobson, A.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5vib.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5vib.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/5vib ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5vib | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40757.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)T1R / References: UniProt: P00517, cAMP-dependent protein kinase |
---|---|
#2: Protein/peptide | Mass: 1973.177 Da / Num. of mol.: 1 / Fragment: UNP residues 6-23 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: Q3SX13 |
#3: Chemical | ChemComp-9D1 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.07 % / Mosaicity: 1.332 ° |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.6 / Details: 15% methanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.37→50 Å / Num. obs: 16232 / % possible obs: 97.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 58.76 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→29.18 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.434 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.278
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.32 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.37→29.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.37→2.53 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
|