+Open data
-Basic information
Entry | Database: PDB / ID: 4yxr | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF PKA IN COMPLEX WITH inhibitor. | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / COMPLEX (PHOSPHOTRANSFERASE-INHIBITOR) complex | ||||||
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 / AMP-activated protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / peptidyl-serine phosphorylation / cellular response to heat / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Schiffer, A. / Wendt, K.U. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: A combination of spin diffusion methods for the determination of protein-ligand complex structural ensembles. Authors: Pilger, J. / Mazur, A. / Monecke, P. / Schreuder, H. / Elshorst, B. / Bartoschek, S. / Langer, T. / Schiffer, A. / Krimm, I. / Wegstroth, M. / Lee, D. / Hessler, G. / Wendt, K.U. / Becker, S. / Griesinger, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yxr.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yxr.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 4yxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yxr_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4yxr_full_validation.pdf.gz | 431.5 KB | Display | |
Data in XML | 4yxr_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 4yxr_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/4yxr ftp://data.pdbj.org/pub/pdb/validation_reports/yx/4yxr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40707.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ALPHA ISOENZYME / Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase |
---|---|
#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ALPHA ISOENZYME / Source: (gene. exp.) Bos taurus (cattle) / Gene: PKIA / Production host: Escherichia coli (E. coli) / References: UniProt: Q3SX13 |
#3: Chemical | ChemComp-0RW / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Protein: Mes-Bis-Tris 30mM pH 6,4, Lithium chloride 75mM, Dithiothreitol 1mM, Ethylenediaminetetraacetic acid disodium salt 0,1mM, Mega 8 0,15mM, PKA 10mg/ml Reservoir: Methanol 22% PH range: 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 30170 / % possible obs: 99.7 % / Redundancy: 5.36 % / Net I/σ(I): 21.08 |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→2 Å / Cross valid method: FREE R-VALUE
| ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→2 Å
|