+Open data
-Basic information
Entry | Database: PDB / ID: 2xyn | |||||||||
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Title | HUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680 | |||||||||
Components | TYROSINE-PROTEIN KINASE ABL2 | |||||||||
Keywords | TRANSFERASE / CELL ADHESION / 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: 2.81 Å | |||||||||
Authors | Salah, E. / Ugochukwu, E. / Elkins, J.M. / Barr, A.J. / Shrestha, B. / Savitsky, P. / Mahajan, P. / Muniz, J.R.C. / Yue, W.W. / Chaikuad, A. ...Salah, E. / Ugochukwu, E. / Elkins, J.M. / Barr, A.J. / Shrestha, B. / Savitsky, P. / Mahajan, P. / Muniz, J.R.C. / Yue, W.W. / Chaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Crystal Structures of Abl-Related Gene (Abl2) in Complex with Imatinib, Tozasertib (Vx-680), and a Type I Inhibitor of the Triazole Carbothioamide Class. Authors: Salah, E. / Ugochukwu, E. / Barr, A.J. / von Delft, F. / Knapp, S. / 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 | 2xyn.cif.gz | 325.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xyn.ent.gz | 266.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xyn ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xyn | HTTPS FTP |
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-Related structure data
Related structure data | 3hmiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 33543.359 Da / Num. of mol.: 3 / Fragment: RESIDUES 243-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: P42684, non-specific protein-tyrosine kinase #2: Chemical | #3: Chemical | ChemComp-VX6 / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Nonpolymer details | CYCLOPROPA | |
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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: 4.2 Å3/Da / Density % sol: 70.69 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.8M SODIUM SUCCINATE, PH 7, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9782 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→41.14 Å / Num. obs: 41549 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.81→2.96 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HMI Resolution: 2.81→147.66 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.886 / SU B: 27.882 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.264 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→147.66 Å
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Refine LS restraints |
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