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Yorodumi- PDB-1a1c: C-SRC (SH2 DOMAIN) COMPLEXED WITH ACE-PHOSPHOTYR-GLU-(N-ME(-(CH2)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a1c | ||||||
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Title | C-SRC (SH2 DOMAIN) COMPLEXED WITH ACE-PHOSPHOTYR-GLU-(N-ME(-(CH2)3-CYCLOPENTYL)) | ||||||
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 1a1c.cif.gz | 63.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a1c.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a1c_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 1a1c_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | 1a1c_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 1a1c_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a1c ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a1c | HTTPS FTP |
-Related structure data
Related structure data | 1a07C 1a08C 1a09C 1a1aC 1a1bC 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: (-0.7933, 0.3005, -0.5295), 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: 539.558 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: 295 K / pH: 4.6 Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M ACETATE, PH 4.6,2M AMMONIUM SULFATE AT 22 C., temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1994 / 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: 2.4→50 Å / Num. obs: 9865 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.4 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SHD Resolution: 2.4→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / σ(F): 2 Details: PARTIALLY REFINED. NO SITE CHAIN DENSITY FOR THE FOLLOWING RESIDUES, THEREFORE MODELLED AS ALA: LYS A 184, ASN A 196, LYS A 198, GLN B 147, LYS B 155, ARG B 159, GLU B 169, LYS B 184, ASN B ...Details: PARTIALLY REFINED. NO SITE CHAIN DENSITY FOR THE FOLLOWING RESIDUES, THEREFORE MODELLED AS ALA: LYS A 184, ASN A 196, LYS A 198, GLN B 147, LYS B 155, ARG B 159, GLU B 169, LYS B 184, ASN B 196, LYS B 198, ASP B 211, LYS B 235. NO DENSITY VISIBLE FOR THE FOLLOWING RESIDUES, THEREFORE NOT INCLUDED IN THE MODEL: MET A 143, ASP A 144, MET B 143, ASP B 144, SER 145.
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Refinement step | Cycle: LAST / Resolution: 2.4→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: 2.4→2.5 Å / Total num. of bins used: 8 / % reflection obs: 83 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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