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Yorodumi- PDB-4o0x: Back pocket flexibility provides group-II PAK selectivity for typ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o0x | ||||||
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Title | Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors | ||||||
Components | Serine/threonine-protein kinase PAK 4 | ||||||
Keywords | transferase/transferase inhibitor / PAK4 / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / RHOG GTPase cycle / cellular response to organic cyclic compound / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / regulation of cell growth / adherens junction / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.483 Å | ||||||
Authors | Rouge, L. / Tam, C. / Wang, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Back Pocket Flexibility Provides Group II p21-Activated Kinase (PAK) Selectivity for Type I 1/2 Kinase Inhibitors. Authors: Staben, S.T. / Feng, J.A. / Lyle, K. / Belvin, M. / Boggs, J. / Burch, J.D. / Chua, C.C. / Cui, H. / Dipasquale, A.G. / Friedman, L.S. / Heise, C. / Koeppen, H. / Kotey, A. / Mintzer, R. / ...Authors: Staben, S.T. / Feng, J.A. / Lyle, K. / Belvin, M. / Boggs, J. / Burch, J.D. / Chua, C.C. / Cui, H. / Dipasquale, A.G. / Friedman, L.S. / Heise, C. / Koeppen, H. / Kotey, A. / Mintzer, R. / Oh, A. / Roberts, D.A. / Rouge, L. / Rudolph, J. / Tam, C. / Wang, W. / Xiao, Y. / Young, A. / Zhang, Y. / Hoeflich, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o0x.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o0x.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/4o0x ftp://data.pdbj.org/pub/pdb/validation_reports/o0/4o0x | 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: 33068.422 Da / Num. of mol.: 1 / Fragment: unp residues 300-591 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli (E. coli) References: UniProt: O96013, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-2OQ / |
#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: 2.93 Å3/Da / Density % sol: 58.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 0.2 M Tri-Potassium citrate and 20% PEG3350 in the reservoir, and drops set up by mixing 1.0 uL of reservoir solution and 1.0 uL of protein, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979403 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2012 |
Radiation | Monochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979403 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. all: 14703 / Num. obs: 14703 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.483→2.492 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.483→44.513 Å / SU ML: 0.44 / σ(F): 1.37 / Phase error: 26.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.701 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.483→44.513 Å
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Refine LS restraints |
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LS refinement shell |
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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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