+Open data
-Basic information
Entry | Database: PDB / ID: 1yol | ||||||
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Title | Crystal structure of Src kinase domain in complex with CGP77675 | ||||||
Components | Proto-oncogene tyrosine-protein kinase Src | ||||||
Keywords | TRANSFERASE / protein tyrosine kinase | ||||||
Function / homology | Function and homology information regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / response to mineralocorticoid / positive regulation of dephosphorylation / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / entry of bacterium into host cell / positive regulation of protein transport / Regulation of gap junction activity / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / regulation of vascular permeability / Activated NTRK2 signals through FYN / positive regulation of integrin activation / negative regulation of focal adhesion assembly / positive regulation of protein processing / skeletal muscle cell proliferation / Signaling by EGFR / : / intestinal epithelial cell development / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / response to acidic pH / focal adhesion assembly / signal complex assembly / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / podosome / regulation of bone resorption / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / branching involved in mammary gland duct morphogenesis / adherens junction organization / DCC mediated attractive signaling / myoblast proliferation / EPH-Ephrin signaling / odontogenesis / negative regulation of mitochondrial depolarization / Ephrin signaling / cellular response to peptide hormone stimulus / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / positive regulation of bone resorption / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / Receptor Mediated Mitophagy / GP1b-IX-V activation signalling / CTLA4 inhibitory signaling / oogenesis / phospholipase activator activity / leukocyte migration / interleukin-6-mediated signaling pathway / GAB1 signalosome / DNA biosynthetic process / Fc-gamma receptor signaling pathway involved in phagocytosis / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / positive regulation of Notch signaling pathway / cellular response to platelet-derived growth factor stimulus / stress fiber assembly / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / negative regulation of hippo signaling / progesterone receptor signaling pathway / regulation of heart rate by cardiac conduction / RUNX2 regulates osteoblast differentiation / dendritic growth cone / Recycling pathway of L1 / stimulatory C-type lectin receptor signaling pathway / PECAM1 interactions / uterus development / phospholipase binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Long-term potentiation / neurotrophin TRK receptor signaling pathway / negative regulation of telomere maintenance via telomerase / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / Signaling by ERBB2 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Breitenlechner, C.B. / Kairies, N.A. / Honold, K. / Scheiblich, S. / Koll, H. / Greiter, E. / Koch, S. / Schaefer, W. / Huber, R. / Engh, R.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structures of active SRC kinase domain complexes Authors: Breitenlechner, C.B. / Kairies, N.A. / Honold, K. / Scheiblich, S. / Koll, H. / Greiter, E. / Koch, S. / Schaefer, W. / Huber, R. / Engh, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yol.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yol.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yol_validation.pdf.gz | 497.5 KB | Display | wwPDB validaton report |
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Full document | 1yol_full_validation.pdf.gz | 504.4 KB | Display | |
Data in XML | 1yol_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1yol_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/1yol ftp://data.pdbj.org/pub/pdb/validation_reports/yo/1yol | HTTPS FTP |
-Related structure data
Related structure data | 1yojC 1yomC 1fmkS 3lckS C: citing same article (ref.) 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
#1: Protein | Mass: 32427.209 Da / Num. of mol.: 2 / Fragment: SRC KINASE DOMAIN / Mutation: S344N, A369S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P12931, EC: 2.7.1.112 #2: Chemical | #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: 2.88 Å3/Da / Density % sol: 57.36 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 31, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 29676 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.3→2.5 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 5.2 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FMK/3LCK hybrid Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.581 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.276 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.462 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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