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Open data
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Basic information
Entry | Database: PDB / ID: 3tz8 | ||||||
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Title | Kinase domain of cSrc in complex with RL104 | ||||||
![]() | Proto-oncogene tyrosine-protein kinase Src![]() | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Type II / ![]() | ||||||
Function / homology | ![]() Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gruetter, C. / Richters, A. / Rauh, D. | ||||||
![]() | ![]() Title: Overcoming Gatekeeper Mutations in cSrc and Abl by Hybrid Compound Design Authors: Richters, A. / Getlik, M. / Gruetter, C. / Schneider, R. / Heuckmann, J.M. / Heynck, S. / Sos, M.L. / Thomas, R.K. / Rauh, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.4 KB | Display | ![]() |
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PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3tz7C ![]() 3tz9C ![]() 3f3vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 32742.711 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residues 251-533 / Mutation: S345C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P00523, ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.74 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 20000, 15% glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 30, 2009 / Details: Dynamically bendable mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. all: 20806 / Num. obs: 20010 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.26 % / Biso Wilson estimate: 33.979 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.91 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3F3V Resolution: 2.7→41.96 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.2509 / WRfactor Rwork: 0.1944 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8142 / SU B: 22.836 / SU ML: 0.241 / SU R Cruickshank DPI: 0.8753 / SU Rfree: 0.3426 / Cross valid method: THROUGHOUT / ESU R Free: 0.337 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.23 Å2 / Biso mean: 27.968 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→41.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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