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Open data
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Basic information
Entry | Database: PDB / ID: 4c36 | ||||||
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Title | PKA-S6K1 Chimera with compound 15e (CCT147581) bound | ||||||
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![]() | TRANSFERASE/INHIBITOR / TRANSFERASE-INHIBITOR COMPLEX / CHIMERA / S6K1 | ||||||
Function / homology | ![]() 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 inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Couty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. ...Couty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. / Barillari, C. / McAndrew, P.C. / Clarke, P.A. / Linardopoulos, S. / Griffin, R.J. / Aherne, G.W. / Raynaud, F.I. / Workman, P. / Jones, K. / van Montfort, R.L.M. | ||||||
![]() | ![]() Title: The discovery of potent ribosomal S6 kinase inhibitors by high-throughput screening and structure-guided drug design. Authors: Couty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. / Barillari, C. / McAndrew, P.C. / Clarke, P.A. / ...Authors: Couty, S. / Westwood, I.M. / Kalusa, A. / Cano, C. / Travers, J. / Boxall, K. / Chow, C.L. / Burns, S. / Schmitt, J. / Pickard, L. / Barillari, C. / McAndrew, P.C. / Clarke, P.A. / Linardopoulos, S. / Griffin, R.J. / Aherne, G.W. / Raynaud, F.I. / Workman, P. / Jones, K. / van Montfort, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.1 KB | Display | ![]() |
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PDB format | ![]() | 132.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739.5 KB | Display | ![]() |
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Full document | ![]() | 739.6 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c33SC ![]() 4c34C ![]() 4c35C ![]() 4c37C ![]() 4c38C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41028.641 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: PKA-S6K1 CHIMERA / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-25 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-ZO9 / |
#4: Chemical | ChemComp-MOH / |
#5: Water | ChemComp-HOH / |
Sequence details | PKA-S6K1 CHIMERA MUTATIONS ARE F54Y, M120L, V123L, L173M AND Q181K |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.25 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: 18 MG/ML PROTEIN IN 25MM MES-BIS-TRIS PH 6.5, 75MM LICL, 0.1MM EDTA, 1MM MEGA-8, 1MM DTT AND 1MM PKI PEPTIDE MIXED 1:1 WITH 8-16% AQUEOUS METHANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→55.17 Å / Num. obs: 31577 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.9 % / Biso Wilson estimate: 27.22 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4C33 Resolution: 1.98→55.17 Å / Cor.coef. Fo:Fc: 0.9559 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.123 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→55.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.04 Å / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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