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Yorodumi- PDB-3lm5: Crystal Structure of human Serine/Threonine Kinase 17B (STK17B) i... -
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-Basic information
Entry | Database: PDB / ID: 3lm5 | ||||||
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Title | Crystal Structure of human Serine/Threonine Kinase 17B (STK17B) in complex with Quercetin | ||||||
Components | Serine/threonine-protein kinase 17B | ||||||
Keywords | TRANSFERASE / STK17B / serine/threonine kinase 17B / DRAK2 / DAP kinase related apoptosis-inducing protein kinase 2 / death-associated protein kinase-related 2 / Structural Genomics / Structural Genomics Consortium / SGC / Apoptosis / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation ...positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Ugochukwu, E. / Soundararajan, M. / Rellos, P. / Fedorov, O. / Phillips, C. / Wang, J. / Hapka, E. / Filippakopoulos, P. / Chaikuad, A. / Pike, A.C.W. ...Ugochukwu, E. / Soundararajan, M. / Rellos, P. / Fedorov, O. / Phillips, C. / Wang, J. / Hapka, E. / Filippakopoulos, P. / Chaikuad, A. / Pike, A.C.W. / Carpenter, L. / Vollmar, M. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. Authors: Picado, A. / Chaikuad, A. / Wells, C.I. / Shrestha, S. / Zuercher, W.J. / Pickett, J.E. / Kwarcinski, F.E. / Sinha, P. / de Silva, C.S. / Zutshi, R. / Liu, S. / Kannan, N. / Knapp, S. / ...Authors: Picado, A. / Chaikuad, A. / Wells, C.I. / Shrestha, S. / Zuercher, W.J. / Pickett, J.E. / Kwarcinski, F.E. / Sinha, P. / de Silva, C.S. / Zutshi, R. / Liu, S. / Kannan, N. / Knapp, S. / Drewry, D.H. / Willson, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lm5.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lm5.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 3lm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lm5_validation.pdf.gz | 721.3 KB | Display | wwPDB validaton report |
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Full document | 3lm5_full_validation.pdf.gz | 722.1 KB | Display | |
Data in XML | 3lm5_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3lm5_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/3lm5 ftp://data.pdbj.org/pub/pdb/validation_reports/lm/3lm5 | HTTPS FTP |
-Related structure data
Related structure data | 6y6fC 6y6hC 6zjfC 7akgC 3ehaS S: Starting model for refinement 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: 37327.086 Da / Num. of mol.: 1 / Fragment: STK17B Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DRAK2, STK17B / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 References: UniProt: O94768, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-QUE / |
#3: 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: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M NaCl; 0.1M BIS-TRIS pH 5.5; 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å |
Detector | Type: MAR225 / Detector: CCD / Date: Dec 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→52.49 Å / Num. obs: 18152 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.29→2.39 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.902 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EHA Resolution: 2.29→52.49 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.051 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.239 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→52.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.285→2.345 Å / Total num. of bins used: 20
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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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