+Open data
-Basic information
Entry | Database: PDB / ID: 2sem | ||||||
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Title | SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR | ||||||
Components |
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Keywords | SIGNALING PROTEIN/INHIBITOR / SH3 DOMAIN / INHIBITORS / PEPTOIDS / PROTEIN-PROTEIN RECOGNITION / PROLINE-RICH MOTIFS / SIGNAL TRANSDUCTION / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling ...Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / PI-3K cascade:FGFR4 / Insulin receptor signalling cascade / MET activates RAS signaling / MET activates PI3K/AKT signaling / RHOU GTPase cycle / FLT3 Signaling / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / PI3K events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / EGFR Transactivation by Gastrin / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of cell projection organization / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / regulation of nematode larval development / EGFR downregulation / Negative regulation of MET activity / Cargo recognition for clathrin-mediated endocytosis / Regulation of signaling by CBL / Clathrin-mediated endocytosis / regulation of vulval development / male genitalia development / COP9 signalosome / muscle organ development / epidermal growth factor receptor binding / regulation of MAPK cascade / phosphotyrosine residue binding / regulation of cell migration / epidermal growth factor receptor signaling pathway / signal transduction / nucleoplasm / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nguyen, J.T. / Turck, C.W. / Cohen, F.E. / Zuckermann, R.N. / Lim, W.A. | ||||||
Citation | Journal: Science / Year: 1998 Title: Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Authors: Nguyen, J.T. / Turck, C.W. / Cohen, F.E. / Zuckermann, R.N. / Lim, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2sem.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2sem.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 2sem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2sem_validation.pdf.gz | 384.5 KB | Display | wwPDB validaton report |
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Full document | 2sem_full_validation.pdf.gz | 384.8 KB | Display | |
Data in XML | 2sem_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 2sem_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/2sem ftp://data.pdbj.org/pub/pdb/validation_reports/se/2sem | HTTPS FTP |
-Related structure data
Related structure data | 1b07C 3semC 1semS 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: (0.0267, -0.9881, 0.1517), Vector: |
-Components
#1: Protein | Mass: 7000.690 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SH3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29355 #2: Protein/peptide | Type: Peptide-like / Class: Inhibitor / Mass: 945.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PEPTIDOMIMETIC INHIBITOR References: 1-acetyl-L-prolyl-L-prolyl-L-prolyl-L-valyl-N-(1-methylethyl)glycyl-L-prolyl-N~5~-[amino(iminio)methyl]-L-ornithyl- N~5~-[amino(iminio)methyl]-L-ornithine #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: 2.05 Å3/Da / Density % sol: 40.13 % | ||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 6144 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.093 |
Reflection shell | Resolution: 2.2→2.29 Å / Redundancy: 4 % / Rsym value: 0.212 / % possible all: 99 |
Reflection | *PLUS Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.212 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SEM Resolution: 2.2→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.29 Å / Total num. of bins used: 8
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