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Yorodumi- PDB-2uw4: Structure of PKA-PKB chimera complexed with 2-(4-(5-methyl-1H-pyr... -
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-Basic information
Entry | Database: PDB / ID: 2uw4 | ||||||
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Title | Structure of PKA-PKB chimera complexed with 2-(4-(5-methyl-1H-pyrazol- 4-yl)-phenyl)-ethylamine | ||||||
Components |
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Keywords | TRANSFERASE / CAMP / KINASE / MYRISTATE / LIPOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / PROTEIN KINASE INHIBITOR / ATP-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION | ||||||
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 / RET signaling / AURKA Activation by TPX2 / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / negative regulation of cAMP-dependent protein kinase activity / VEGFA-VEGFR2 Pathway / negative regulation of cAMP/PKA signal transduction / PKA activation / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / 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 / negative regulation of protein import into nucleus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein phosphorylation / protein domain specific binding / 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 Å | ||||||
Authors | Davies, T.G. / Saxty, G. / Woodhead, S.J. / Berdini, V. / Verdonk, M.L. / Wyatt, P.G. / Boyle, R.G. / Barford, D. / Downham, R. / Garrett, M.D. / Carr, R.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Identification of Inhibitors of Protein Kinase B Using Fragment-Based Lead Discovery Authors: Saxty, G. / Woodhead, S.J. / Berdini, V. / Davies, T.G. / Verdonk, M.L. / Wyatt, P.G. / Boyle, R.G. / Barford, D. / Downham, R. / Garrett, M.D. / Carr, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uw4.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uw4.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 2uw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uw4_validation.pdf.gz | 452 KB | Display | wwPDB validaton report |
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Full document | 2uw4_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 2uw4_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 2uw4_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uw4 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uw4 | HTTPS FTP |
-Related structure data
Related structure data | 2uw3C 2uw5C 2uw6C 2uw7C 2uw8C 2uw9C C: citing same article (ref.) |
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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: 40830.617 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00517, cAMP-dependent protein kinase |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-24 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P61925 |
#3: Chemical | ChemComp-L15 / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, VAL 104 TO THR ENGINEERED RESIDUE IN CHAIN A, VAL 123 TO ALA ...ENGINEERED |
Has protein modification | Y |
Sequence details | 4 RESIDUES OF THE WILD-TYPE PKA SEQUENCE HAVE BEEN MUTATED TO THE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.5 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.3 Å / Num. obs: 28339 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.7 / % possible all: 91.4 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019G / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.046 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.32 Å
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