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- PDB-1bm2: GRB2-SH2 DOMAIN IN COMPLEX WITH CYCLO-[N-ALPHA-ACETYL-L-THI ALYSY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bm2 | ||||||
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Title | GRB2-SH2 DOMAIN IN COMPLEX WITH CYCLO-[N-ALPHA-ACETYL-L-THI ALYSYL-O-PHOSPHOTYROSYL-VALYL-ASPARAGYL-VALYL-PROLYL] (PKF273-791) | ||||||
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![]() | HORMONE/GROWTH FACTOR / SH2 DOMAIN / SIGNAL TRANSDUCTION / ADAPTOR PROTEIN / RAS PATHWAY / CYCLIC PEPTIDE / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | ![]() : / Signaling by FGFR3 fusions in cancer / : / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / : / ERBB2 signaling pathway / entry of bacterium into host cell / branching involved in labyrinthine layer morphogenesis ...: / Signaling by FGFR3 fusions in cancer / : / anatomical structure formation involved in morphogenesis / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / : / ERBB2 signaling pathway / entry of bacterium into host cell / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / membrane organization / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / interleukin-15-mediated signaling pathway / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / vesicle membrane / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / positive regulation of Ras protein signal transduction / MET activates PTPN11 / Signaling by LTK / MET activates RAP1 and RAC1 / Costimulation by the CD28 family / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / natural killer cell mediated cytotoxicity / Regulation of KIT signaling / epidermal growth factor receptor binding / leukocyte migration / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / Fc-gamma receptor signaling pathway involved in phagocytosis / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of epidermal growth factor receptor signaling pathway / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / endodermal cell differentiation / PI-3K cascade:FGFR1 / Fc-epsilon receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of MAPK cascade / neurotrophin TRK receptor signaling pathway / RHOU GTPase cycle / PI3K events in ERBB2 signaling / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / insulin receptor substrate binding / PI3K Cascade / SHC1 events in ERBB4 signaling / Signalling to RAS / RHO GTPases Activate WASPs and WAVEs / signal transduction in response to DNA damage / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signal attenuation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / T cell costimulation / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Signaling by FGFR1 in disease / viral process / GRB2 events in ERBB2 signaling / ephrin receptor binding / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / SHC1 events in ERBB2 signaling / Downstream signal transduction Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rondeau, J.M. / Zurini, M. | ||||||
![]() | ![]() Title: Structural and conformational requirements for high-affinity binding to the SH2 domain of Grb2(1). Authors: Ettmayer, P. / France, D. / Gounarides, J. / Jarosinski, M. / Martin, M.S. / Rondeau, J.M. / Sabio, M. / Topiol, S. / Weidmann, B. / Zurini, M. / Bair, K.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.5 KB | Display | ![]() |
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PDB format | ![]() | 24.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bmbSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13577.362 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 842.896 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: ACE: N-TERMINAL ACETYL GROUP PTR: L-PHOSPHOTYROSINE |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN (15MG/ML IN 100MM SODIUM CHLORIDE, 0.02% SODIUM AZIDE) WAS CRYSTALLIZED FROM 30% SATURATED AMMONIUM SULFATE, 100MM SODIUM HEPES PH 7.0, IN PRESENCE OF A 2-FOLD EXCESS OF LIGAND | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 19, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→8 Å / Num. obs: 7262 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.1 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BMB Resolution: 2.1→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 27.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.358 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.281 |