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Yorodumi- PDB-6c0t: Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6c0t | ||||||
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Title | Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain bound with N46 | ||||||
Components | cGMP-dependent protein kinase 1 | ||||||
Keywords | transferase/transferase inhibitor / Serine/threonine protein kinases (EC 2.7.11.12) / TRANSFERASE / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm ...negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / negative regulation of vascular associated smooth muscle cell migration / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / regulation of GTPase activity / mitogen-activated protein kinase p38 binding / cGMP-mediated signaling / dendrite development / cGMP effects / negative regulation of vascular associated smooth muscle cell proliferation / spermatid development / cGMP binding / calcium channel regulator activity / forebrain development / protein kinase A signaling / acrosomal vesicle / cerebellum development / neuron migration / sarcolemma / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Qin, L. / Sankaran, B. / Kim, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural basis for selective inhibition of human PKG I alpha by the balanol-like compound N46. Authors: Qin, L. / Sankaran, B. / Aminzai, S. / Casteel, D.E. / Kim, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c0t.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c0t.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 6c0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6c0t_validation.pdf.gz | 726 KB | Display | wwPDB validaton report |
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Full document | 6c0t_full_validation.pdf.gz | 729.9 KB | Display | |
Data in XML | 6c0t_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6c0t_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/6c0t ftp://data.pdbj.org/pub/pdb/validation_reports/c0/6c0t | HTTPS FTP |
-Related structure data
Related structure data | 6c0uC 6bg2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39473.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N46 / Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Plasmid: pBlueBacHis2A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13976, cGMP-dependent protein kinase |
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#2: Chemical | ChemComp-EE4 / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-PGE / |
#5: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24%w/v PEG1500, 20%v/v glycerol, 3% w/v Trimethylamine N-oxide dihydrate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→43.62 Å / Num. obs: 25870 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.98→2.03 Å / Rmerge(I) obs: 0.904 / CC1/2: 0.912 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BG2 Resolution: 1.98→42.865 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→42.865 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -22.6016 Å / Origin y: 18.2327 Å / Origin z: 6.4865 Å
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Refinement TLS group | Selection details: all |