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Yorodumi- PDB-1a1b: C-SRC (SH2 DOMAIN) COMPLEXED WITH ACE-PHOSPHOTYR-GLU-(N,N-DIPENTY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a1b | ||||||
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Title | C-SRC (SH2 DOMAIN) COMPLEXED WITH ACE-PHOSPHOTYR-GLU-(N,N-DIPENTYL AMINE) | ||||||
Components |
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Keywords | COMPLEX (TRANSFERASE/PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) / COMPLEX (TRANSFERASE-PEPTIDE) complex | ||||||
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 / positive regulation of dephosphorylation / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / ERBB2 signaling pathway / regulation of epithelial cell migration / positive regulation of protein transport / Regulation of gap junction activity / regulation of vascular permeability / entry of bacterium into host cell / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / positive regulation of integrin activation / Activated NTRK2 signals through FYN / negative regulation of focal adhesion assembly / skeletal muscle cell proliferation / positive regulation of protein processing / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / Activated NTRK3 signals through PI3K / connexin binding / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / response to acidic pH / podosome / negative regulation of telomere maintenance via telomerase / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / DCC mediated attractive signaling / negative regulation of mitochondrial depolarization / adherens junction organization / osteoclast development / myoblast proliferation / EPH-Ephrin signaling / Ephrin signaling / odontogenesis / cellular response to peptide hormone stimulus / Signal regulatory protein family interactions / cellular response to fatty acid / regulation of early endosome to late endosome transport / MET activates PTK2 signaling / oogenesis / Receptor Mediated Mitophagy / GP1b-IX-V activation signalling / Regulation of KIT signaling / Signaling by ALK / postsynaptic specialization, intracellular component / CTLA4 inhibitory signaling / Signaling by EGFR / phospholipase activator activity / leukocyte migration / DNA biosynthetic process / EPHA-mediated growth cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / interleukin-6-mediated signaling pathway / p130Cas linkage to MAPK signaling for integrins / negative regulation of hippo signaling / positive regulation of epithelial cell migration / positive regulation of Notch signaling pathway / stress fiber assembly / negative regulation of telomerase activity / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / regulation of heart rate by cardiac conduction / Recycling pathway of L1 / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / dendritic growth cone / stimulatory C-type lectin receptor signaling pathway / uterus development / PECAM1 interactions / phospholipase binding / neurotrophin TRK receptor signaling pathway / Long-term potentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / FCGR activation / EPH-ephrin mediated repulsion of cells / negative regulation of anoikis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shewchuk, L. / Jordan, S. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Peptide ligands of pp60(c-src) SH2 domains: a thermodynamic and structural study. Authors: Charifson, P.S. / Shewchuk, L.M. / Rocque, W. / Hummel, C.W. / Jordan, S.R. / Mohr, C. / Pacofsky, G.J. / Peel, M.R. / Rodriguez, M. / Sternbach, D.D. / Consler, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a1b.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a1b.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a1b ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a1b | HTTPS FTP |
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-Related structure data
Related structure data | 1a07C 1a08C 1a09C 1a1aC 1a1cC 1a1eC 1shdS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.7806, 0.308, -0.5439), Vector: |
-Components
#1: Protein | Mass: 12303.886 Da / Num. of mol.: 2 / Fragment: SH2 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: SRC / Plasmid: PET11B / Cellular location (production host): CYTOPLASM / Gene (production host): SRC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P12931, EC: 2.7.1.112 #2: Protein/peptide | Mass: 555.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #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: 2.6 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8 Details: PROTEIN WAS CRYSTALLIZED FROM 2M AMMONIUM SULFATE AT 4 DEGREES C., pH 8.0, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 12571 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.1 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SHD Resolution: 2.2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / σ(F): 2 / Details: PARTIALLY REFINED
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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