+Open data
-Basic information
Entry | Database: PDB / ID: 7cmb | ||||||
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Title | Crystal Structure of PAK4 in complex with inhibitor 41 | ||||||
Components | Serine/threonine-protein kinase PAK 4 | ||||||
Keywords | TRANSFERASE / ATP binding pocket | ||||||
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 / cellular response to organic cyclic compound / RHOG GTPase cycle / 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 / protein serine kinase activity / focal adhesion / 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: 2.592 Å | ||||||
Authors | Zhao, F. / Li, H. | ||||||
Citation | Journal: to be published Title: Discovery of 6-ethynyl-1H-indole-3-carboxamide Derivatives as Highly Potent and Selective p21-Activated Kinase 4 (PAK4) Inhibitors Authors: Song, P. / Zhao, F. / Cheng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cmb.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cmb.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 7cmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/7cmb ftp://data.pdbj.org/pub/pdb/validation_reports/cm/7cmb | HTTPS FTP |
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-Related structure data
Related structure data | 7cp3C 7cp4C 5xvfS 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: 33098.449 Da / Num. of mol.: 1 / Fragment: PAK4 Kinase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Plasmid: pSUMOH10 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O96013, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-G5X / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.78 % / Mosaicity: 1.254 ° / Mosaicity esd: 0.019 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2019 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.592→50 Å / Num. obs: 12343 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.053 / Rrim(I) all: 0.155 / Χ2: 1.926 / Net I/σ(I): 6.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XVF Resolution: 2.592→26.063 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.58 / 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 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.78 Å2 / Biso mean: 75.003 Å2 / Biso min: 39.97 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.592→26.063 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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