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Yorodumi- PDB-7pid: Protein kinase A catalytic subunit in complex with PKI5-24 and EN060 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pid | |||||||||
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Title | Protein kinase A catalytic subunit in complex with PKI5-24 and EN060 | |||||||||
Components |
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Keywords | TRANSFERASE / Protein Kinase / Ligand complex | |||||||||
Function / homology | Function and homology information regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Cricetulus griseus (Chinese hamster) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.496 Å | |||||||||
Authors | Glinca, S. / Mueller, J.M. / Ruf, M. / Merkl, S. | |||||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Magnet for the Needle in Haystack: "Crystal Structure First" Fragment Hits Unlock Active Chemical Matter Using Targeted Exploration of Vast Chemical Spaces. Authors: Muller, J. / Klein, R. / Tarkhanova, O. / Gryniukova, A. / Borysko, P. / Merkl, S. / Ruf, M. / Neumann, A. / Gastreich, M. / Moroz, Y.S. / Klebe, G. / Glinca, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pid.cif.gz | 298.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pid.ent.gz | 201.8 KB | Display | PDB format |
PDBx/mmJSON format | 7pid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/7pid ftp://data.pdbj.org/pub/pdb/validation_reports/pi/7pid | HTTPS FTP |
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-Related structure data
Related structure data | 7pieC 7pifC 7pigC 7pihC 7pnsC 5m6yS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41193.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Organ: Ovary Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P25321, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PKI5-24, the last two residues are disordered / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248 |
#3: Chemical | ChemComp-7QI / |
#4: Chemical | ChemComp-MPD / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: Protein at 8 mg/mL in 100 mM Mes-Bis-Tris pH 6.9, 75 mM Lithium chloride, 1 mM DTT, 100 mM Sodium-EDTA. Master-Mix: 540 uL of protein + 15 uL 10 mM Mega8 in Water + 45 uL 10 mM PKI5-24 in ...Details: Protein at 8 mg/mL in 100 mM Mes-Bis-Tris pH 6.9, 75 mM Lithium chloride, 1 mM DTT, 100 mM Sodium-EDTA. Master-Mix: 540 uL of protein + 15 uL 10 mM Mega8 in Water + 45 uL 10 mM PKI5-24 in protein-buffer. 70 % Master-Mix mixed with 30 % 50 mM ligand in DMSO before setting of drops. 15-24 % Methanol/Water in Reservoir. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033193 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033193 Å / Relative weight: 1 |
Reflection | Resolution: 1.496→45.7610803693 Å / Num. obs: 76966 / % possible obs: 99.6 % / Redundancy: 13.08 % / Biso Wilson estimate: 20.1617100127 Å2 / CC1/2: 0.999 / Rsym value: 0.053 / Net I/σ(I): 27.22 |
Reflection shell | Resolution: 1.496→1.58 Å / Redundancy: 13 % / Mean I/σ(I) obs: 5.86 / Num. unique obs: 12087 / CC1/2: 0.956 / Rsym value: 0.5 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M6Y Resolution: 1.496→45.7610803693 Å / SU ML: 0.089950383788 / Cross valid method: FREE R-VALUE / σ(F): 1.38082386903 / Phase error: 13.1228058308 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4098029108 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.496→45.7610803693 Å
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Refine LS restraints |
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LS refinement shell |
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