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Yorodumi- PDB-7b8w: Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b8w | ||||||
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Title | Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 | ||||||
Components | LIM domain kinase 1 | ||||||
Keywords | SIGNALING PROTEIN / LIMK1 Kinase domain / inhibitor | ||||||
Function / homology | Function and homology information positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion ...positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / positive regulation of axon extension / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / heat shock protein binding / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / lamellipodium / nervous system development / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / neuron projection / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / signal transduction / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Lee, H. / Yosaatmadja, Y. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Elkins, J.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470 Authors: Lee, H. / Yosaatmadja, Y. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Elkins, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b8w.cif.gz | 226.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b8w.ent.gz | 179.1 KB | Display | PDB format |
PDBx/mmJSON format | 7b8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/7b8w ftp://data.pdbj.org/pub/pdb/validation_reports/b8/7b8w | HTTPS FTP |
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-Related structure data
Related structure data | 5nxcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 35994.773 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P53667, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-T3B / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.38 Å3/Da / Density % sol: 48.33 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium Citrate dibasic, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→51.2 Å / Num. obs: 33406 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.091 / Rrim(I) all: 0.239 / Net I/σ(I): 7 / Num. measured all: 225877 / Scaling rejects: 24 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NXC Resolution: 2.8→50.15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.858 / SU B: 18.604 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.53 Å2 / Biso mean: 45.413 Å2 / Biso min: 24.34 Å2
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Refinement step | Cycle: final / Resolution: 2.8→50.15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3903 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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