+Open data
-Basic information
Entry | Database: PDB / ID: 5d11 | ||||||
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Title | Kinase domain of cSrc in complex with RL235 | ||||||
Components | Proto-oncogene tyrosine-protein kinase Src | ||||||
Keywords | TRANSFERASE / kinase inhibitor / drug resistance | ||||||
Function / homology | Function and homology information Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / regulation of cell cycle / endosome membrane / cell adhesion / innate immune response / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Becker, C. / Gruetter, C. / Engel, J. / Rauh, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach. Authors: Engel, J. / Richters, A. / Getlik, M. / Tomassi, S. / Keul, M. / Termathe, M. / Lategahn, J. / Becker, C. / Mayer-Wrangowski, S. / Grutter, C. / Uhlenbrock, N. / Krull, J. / Schaumann, N. / ...Authors: Engel, J. / Richters, A. / Getlik, M. / Tomassi, S. / Keul, M. / Termathe, M. / Lategahn, J. / Becker, C. / Mayer-Wrangowski, S. / Grutter, C. / Uhlenbrock, N. / Krull, J. / Schaumann, N. / Eppmann, S. / Kibies, P. / Hoffgaard, F. / Heil, J. / Menninger, S. / Ortiz-Cuaran, S. / Heuckmann, J.M. / Tinnefeld, V. / Zahedi, R.P. / Sos, M.L. / Schultz-Fademrecht, C. / Thomas, R.K. / Kast, S.M. / Rauh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d11.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d11.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/5d11 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/5d11 | HTTPS FTP |
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-Related structure data
Related structure data | 5d10C 5d12C 2oiqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32772.801 Da / Num. of mol.: 2 / Mutation: T338M, S345C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli) References: UniProt: P00523, non-specific protein-tyrosine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.085-0.125 mM MES, 9-11.5 % PEG20000 / PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→45 Å / Num. obs: 33021 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.48 % / Biso Wilson estimate: 41.021 Å2 / Rmerge F obs: 0.09 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.078 / Χ2: 1.001 / Net I/σ(I): 15.35 / Num. measured all: 115170 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OIQ Resolution: 2.3→43.54 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.86 / SU B: 7.238 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.23 / 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: 110.48 Å2 / Biso mean: 40.712 Å2 / Biso min: 14.58 Å2
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Refinement step | Cycle: final / Resolution: 2.3→43.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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