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Yorodumi- PDB-6e9l: Crystal structure of Protein Kinase A in complex with the PKI pep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e9l | ||||||
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Title | Crystal structure of Protein Kinase A in complex with the PKI peptide and a pyridinylbenzamide based inhibitor | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase A / kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE 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 / 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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of protein import into nucleus / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / 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 / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Judge, R.A. / Hobson, A.D. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Identification of Selective Dual ROCK1 and ROCK2 Inhibitors Using Structure Based Drug Design. Authors: Hobson, A.D. / Judge, R.A. / Aguirre, A.L. / Brown, B.S. / Cui, Y. / Ding, P. / Dominguez, E. / DiGiammarino, E. / Egan, D.A. / Freiberg, G.M. / Gopalakrishnan, S.M. / Harris, C.M. / Honore, ...Authors: Hobson, A.D. / Judge, R.A. / Aguirre, A.L. / Brown, B.S. / Cui, Y. / Ding, P. / Dominguez, E. / DiGiammarino, E. / Egan, D.A. / Freiberg, G.M. / Gopalakrishnan, S.M. / Harris, C.M. / Honore, M.P. / Kage, K.L. / Kapecki, N.J. / Ling, C. / Ma, J. / Mack, H. / Mamo, M. / Maurus, S. / McRae, B. / Moore, N.S. / Mueller, B.K. / Mueller, R. / Namovic, M.T. / Patel, K. / Pratt, S.D. / Putman, C.B. / Queeney, K.L. / Sarris, K.K. / Schaffter, L.M. / Stoll, V.S. / Vasudevan, A. / Wang, L. / Wang, L. / Wirthl, W. / Yach, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e9l.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e9l.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 6e9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/6e9l ftp://data.pdbj.org/pub/pdb/validation_reports/e9/6e9l | HTTPS FTP |
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-Related 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: 40837.609 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) / References: UniProt: P00517, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 1973.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925 |
#3: Chemical | ChemComp-J0P / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 5 to 27% Methanol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jan 7, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 12483 / % possible obs: 98.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 74.9 Å2 / Rmerge(I) obs: 0.177 / Χ2: 1.49 / Net I/σ(I): 4.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→37.24 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.405
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Displacement parameters | Biso max: 130.78 Å2 / Biso mean: 50.81 Å2 / Biso min: 18.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→37.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 28
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