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Yorodumi- PDB-3lcs: Crystal Structure of the Anaplastic Lymphoma Kinase Catalytic Domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lcs | ||||||
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Title | Crystal Structure of the Anaplastic Lymphoma Kinase Catalytic Domain | ||||||
Components | ALK tyrosine kinase receptor | ||||||
Keywords | TRANSFERASE / kinase domain / ATP-binding / Glycoprotein / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Proto-oncogene / Receptor / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / response to environmental enrichment / ALK mutants bind TKIs / swimming behavior / positive regulation of dendrite development / regulation of neuron differentiation / adult behavior / Signaling by ALK / neuron development / negative regulation of lipid catabolic process / energy homeostasis / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / hippocampus development / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ALK fusions and activated point mutants / receptor protein-tyrosine kinase / heparin binding / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / regulation of apoptotic process / protein tyrosine kinase activity / protein autophosphorylation / receptor complex / phosphorylation / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Lee, C.C. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Crystal structure of the ALK (anaplastic lymphoma kinase) catalytic domain. Authors: Lee, C.C. / Jia, Y. / Li, N. / Sun, X. / Ng, K. / Ambing, E. / Gao, M.Y. / Hua, S. / Chen, C. / Kim, S. / Michellys, P.Y. / Lesley, S.A. / Harris, J.L. / Spraggon, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lcs.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lcs.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/3lcs ftp://data.pdbj.org/pub/pdb/validation_reports/lc/3lcs | HTTPS FTP |
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-Related structure data
Related structure data | 3l9pSC 3lctC 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: 38641.324 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN residues 1072-1410 / Mutation: S1281G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALK / Plasmid: pFastBacHT / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UM73, receptor protein-tyrosine kinase | ||
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#2: Chemical | ChemComp-STU / | ||
#3: Chemical | #4: 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: 2.03 Å3/Da / Density % sol: 39.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 16.0% polyethylene glycol 3350, 2.0% tacsimate pH 8.0, 0.1M tris hydrochloride pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 29513 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.088 / Rsym value: 0.063 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.831 / Rsym value: 0.878 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L9P Resolution: 1.95→52.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.833 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 35.238 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→52.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -14.0045 Å / Origin y: 10.3164 Å / Origin z: -16.425 Å
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