+Open data
-Basic information
Entry | Database: PDB / ID: 3gvu | ||||||
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Title | The crystal structure of human ABL2 in complex with GLEEVEC | ||||||
Components | Tyrosine-protein kinase ABL2 | ||||||
Keywords | TRANSFERASE / Tyrosine kinase / ABL / Abelson murine leukemia viral oncogene / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion ...positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / : / cellular response to retinoic acid / Negative regulation of FLT3 / RAC1 GTPase cycle / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / regulation of autophagy / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein modification process / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / actin filament binding / actin cytoskeleton / manganese ion binding / positive regulation of cytosolic calcium ion concentration / regulation of apoptotic process / protein tyrosine kinase activity / cell adhesion / protein kinase activity / magnesium ion binding / signal transduction / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Ugochukwu, E. / Salah, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Chaikuad, A. / Filippakopoulos, P. / Roos, A. / Pike, A.C.W. ...Ugochukwu, E. / Salah, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Chaikuad, A. / Filippakopoulos, P. / Roos, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of human ABL2 in complex with GLEEVEC Authors: Salah, E. / Ugochukwu, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gvu.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gvu.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gvu ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gvu | HTTPS FTP |
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-Related structure data
Related structure data | 1fpuS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33543.359 Da / Num. of mol.: 1 / Fragment: Protein kinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABL2 / Plasmid: pFB-LIC-Bse / Cell line (production host): High5 Insect cell / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P42684, non-specific protein-tyrosine kinase | ||
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#2: Chemical | #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: 2.88 Å3/Da / Density % sol: 57.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG3350, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.88 Å |
Detector | Type: MAR225 / Detector: CCD / Date: Jan 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→43.9 Å / Num. obs: 24490 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 3.2 / Num. unique all: 12308 / Rsym value: 0.445 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FPU.pdb Resolution: 2.05→43.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.08 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 16.411 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→43.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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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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