+Open data
-Basic information
Entry | Database: PDB / ID: 4p9v | ||||||||||||
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Title | Grb2 SH2 complexed with a pTyr-Ac6cN-Asn tripeptide | ||||||||||||
Components |
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Keywords | Signaling Protein/Antagonist / Grb2 SH2 / Cation-Pi Interaction / Signaling Protein-Antagonist complex | ||||||||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / vesicle membrane / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / vesicle membrane / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / MET activates RAP1 and RAC1 / Costimulation by the CD28 family / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / regulation of MAPK cascade / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / PI3K events in ERBB2 signaling / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / SHC1 events in ERBB4 signaling / Signalling to RAS / RHO GTPases Activate WASPs and WAVEs / fibroblast growth factor receptor signaling pathway / signal transduction in response to DNA damage / SHC-related events triggered by IGF1R / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Signaling by FGFR1 in disease / 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 / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / InlB-mediated entry of Listeria monocytogenes into host cell / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cellular response to ionizing radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / FCERI mediated MAPK activation / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / FCGR3A-mediated phagocytosis / EGFR downregulation / Negative regulation of FGFR1 signaling / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / Spry regulation of FGF signaling Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||||||||
Authors | Clements, J.H. / Martin, S.F. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2014 Title: Protein-ligand interactions: Probing the energetics of a putative cation-pi interaction. Authors: Myslinski, J.M. / Clements, J.H. / Martin, S.F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p9v.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p9v.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 4p9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p9v_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 4p9v_full_validation.pdf.gz | 432.1 KB | Display | |
Data in XML | 4p9v_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 4p9v_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/4p9v ftp://data.pdbj.org/pub/pdb/validation_reports/p9/4p9v | HTTPS FTP |
-Related structure data
Related structure data | 4p9zC 3s8oS 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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-Components
#1: Protein | Mass: 13758.543 Da / Num. of mol.: 1 / Fragment: UNP residues 53-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P62993 |
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#2: Protein/peptide | Mass: 651.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.66 Å3/Da / Density % sol: 25.83 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride, 30% w/v polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 11451 / % possible obs: 90.3 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 19.2 / % possible all: 99.8 |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S8O Resolution: 1.64→39.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 1.726 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.403 Å2
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Refinement step | Cycle: 1 / Resolution: 1.64→39.13 Å
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Refine LS restraints |
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