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Yorodumi- PDB-5ime: Crystal structure of P21-activated kinase 1 (PAK1) in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 5ime | ||||||
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Title | Crystal structure of P21-activated kinase 1 (PAK1) in complex with compound 9 | ||||||
Components | Serine/threonine-protein kinase PAK 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway / DSCAM interactions / RHOV GTPase cycle / regulation of axonogenesis / branching morphogenesis of an epithelial tube / Fc-gamma receptor signaling pathway involved in phagocytosis / RHOJ GTPase cycle / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / Generation of second messenger molecules / intercalated disc / Smooth Muscle Contraction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / localization / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / positive regulation of stress fiber assembly / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / collagen binding / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / wound healing / G beta:gamma signalling through CDC42 / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cell-cell junction / cell migration / lamellipodium / positive regulation of peptidyl-serine phosphorylation / chromosome / actin cytoskeleton organization / nuclear membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of cell migration / intracellular signal transduction / chromatin remodeling / positive regulation of protein phosphorylation / axon / phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / apoptotic process / DNA damage response / positive regulation of cell population proliferation / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.217 Å | ||||||
Authors | Li, D. / Wang, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Chemically Diverse Group I p21-Activated Kinase (PAK) Inhibitors Impart Acute Cardiovascular Toxicity with a Narrow Therapeutic Window. Authors: Rudolph, J. / Murray, L.J. / Ndubaku, C.O. / O'Brien, T. / Blackwood, E. / Wang, W. / Aliagas, I. / Gazzard, L. / Crawford, J.J. / Drobnick, J. / Lee, W. / Zhao, X. / Hoeflich, K.P. / Favor, ...Authors: Rudolph, J. / Murray, L.J. / Ndubaku, C.O. / O'Brien, T. / Blackwood, E. / Wang, W. / Aliagas, I. / Gazzard, L. / Crawford, J.J. / Drobnick, J. / Lee, W. / Zhao, X. / Hoeflich, K.P. / Favor, D.A. / Dong, P. / Zhang, H. / Heise, C.E. / Oh, A. / Ong, C.C. / La, H. / Chakravarty, P. / Chan, C. / Jakubiak, D. / Epler, J. / Ramaswamy, S. / Vega, R. / Cain, G. / Diaz, D. / Zhong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ime.cif.gz | 243.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ime.ent.gz | 195.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ime.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/5ime ftp://data.pdbj.org/pub/pdb/validation_reports/im/5ime | HTTPS FTP |
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-Related structure data
Related structure data | 4o0rS 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: 33544.504 Da / Num. of mol.: 2 / Fragment: residues 249-545 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Production host: Escherichia coli (E. coli) References: UniProt: Q13153, non-specific serine/threonine protein kinase #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: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium ...Details: crystals were grown at 19 C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 30976 / % possible obs: 98.9 % / Redundancy: 3.6 % / Net I/σ(I): 3.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O0R Resolution: 2.217→37.624 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.9 / Phase error: 33.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.217→37.624 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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