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Yorodumi- PDB-1szm: DUAL BINDING MODE OF BISINDOLYLMALEIMIDE 2 TO PROTEIN KINASE A (PKA) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1szm | ||||||
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Title | DUAL BINDING MODE OF BISINDOLYLMALEIMIDE 2 TO PROTEIN KINASE A (PKA) | ||||||
Components | cAMP-dependent protein kinase, alpha-catalytic subunitCAMP-dependent pathway | ||||||
Keywords | TRANSFERASE / PKA / PKC / bisindolyl maleimide 2 / LY333531 / selectivity / surrogate kinase / amino acid residue exchange | ||||||
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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins / AMP-activated protein kinase activity / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / 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 / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gassel, M. / Breitenlechner, C.B. / Koenig, N. / Huber, R. / Engh, R.A. / Bossemeyer, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed orientations to different conformations of protein kinase a. Authors: Gassel, M. / Breitenlechner, C.B. / Koenig, N. / Huber, R. / Engh, R.A. / Bossemeyer, D. #1: Journal: Structure / Year: 1997 Title: Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential. Authors: Prade, L. / Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D. | ||||||
History |
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Remark 600 | HETEROGEN Atom names used for BIM2 in this entry were chosen to comply with PDB ENTRY 1UU3. They ...HETEROGEN Atom names used for BIM2 in this entry were chosen to comply with PDB ENTRY 1UU3. They correspond to atom names used in the original CITATION AND REFERENCE 1 in the following manner: CAA=C3, CAB=C2, CAC=C1, CAD=C23, CAE=C5, CAF=C4, CAG=C22, NAH=N6, CAI=C21, CAJ=C17, CAK=C16, CAL=C8, CAM=C15, CAN=C10, NAO=N9, CAP=C14, CAQ=C13, CAR=C12, CAS=C11, CAT=C20, NAU=N19, CAV=C18, CAW=C7, OAX=O32, CAY=C24 , OAZ=O33, CBA=C25, CBB=C26, NBC=N30, CBD=C31, CBE=C27, CBF=C28, CBG=C29, |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1szm.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1szm.ent.gz | 113.1 KB | Display | PDB format |
PDBx/mmJSON format | 1szm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/1szm ftp://data.pdbj.org/pub/pdb/validation_reports/sz/1szm | HTTPS FTP |
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-Related structure data
Related structure data | 1stcS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40777.426 Da / Num. of mol.: 2 / Mutation: V123A, L173M, Q181K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Plasmid: pT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P00517, EC: 2.7.1.37 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: LiCl, MesBisTris, methanol, MEGA-8, PKI(5-24), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 11, 2002 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→24.7 Å / Num. all: 31110 / Num. obs: 30100 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.099 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.5→2.64 Å / % possible obs: 99.9 % / Redundancy: 5 % / Mean I/σ(I) obs: 1 / Rsym value: 0.571 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1STC Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.441 / SU ML: 0.257 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.505 / ESU R Free: 0.318 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.536 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20 /
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