+Open data
-Basic information
Entry | Database: PDB / ID: 3f6x | ||||||
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Title | c-Src kinase domain in complex with small molecule inhibitor | ||||||
Components | Proto-oncogene tyrosine-protein kinase Src | ||||||
Keywords | TRANSFERASE / Kinase / ATP-Binding / Alternative splicing / Lipoprotein / Myristate / Nucleotide-binding / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase | ||||||
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 / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / 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 / endosome membrane / cell adhesion / regulation of cell cycle / cell cycle / phosphorylation / innate immune response / focal adhesion / signaling receptor binding / 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: 2.35 Å | ||||||
Authors | Seeliger, M.A. / Statsuk, A.V. / Maly, D.J. / Patrick, P.Z. / Kuriyan, J. / Shokat, K.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Tuning a three-component reaction for trapping kinase substrate complexes. Authors: Statsuk, A.V. / Maly, D.J. / Seeliger, M.A. / Fabian, M.A. / Biggs, W.H. / Lockhart, D.J. / Zarrinkar, P.P. / Kuriyan, J. / Shokat, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f6x.cif.gz | 225.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f6x.ent.gz | 181.6 KB | Display | PDB format |
PDBx/mmJSON format | 3f6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f6x_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3f6x_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3f6x_validation.xml.gz | 45.6 KB | Display | |
Data in CIF | 3f6x_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/3f6x ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f6x | HTTPS FTP |
-Related structure data
Related structure data | 2oiqS 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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-Components
#1: Protein | Mass: 32726.645 Da / Num. of mol.: 4 / Fragment: UNP residues 251-533 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 References: UniProt: P00523, non-specific protein-tyrosine kinase #2: Chemical | ChemComp-IHH / [ #3: 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: 59.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.5, 10 % glycerol, 25 mM ammonium acetate, 50 mM sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 58518 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.063 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 5894 / Rsym value: 0.212 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2OIQ Resolution: 2.35→34.99 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.6 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→34.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.43 Å
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