+Open data
-Basic information
Entry | Database: PDB / ID: 1b07 | ||||||
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Title | CRK SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR | ||||||
Components |
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Keywords | SH3 DOMAIN / INHIBITORS / PEPTOIDS / PROTEIN-PROTEIN RECOGNITION / PROLINE-RICH MOTIFS / SIGNAL TRANSDUCTION | ||||||
Function / homology | Function and homology information Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / SHC-related events triggered by IGF1R ...Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / SHC-related events triggered by IGF1R / SOS-mediated signalling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates RAS signaling / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / Tie2 Signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Interleukin-15 signaling / FLT3 Signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / ARMS-mediated activation / MET activates RAP1 and RAC1 / MET receptor recycling / response to hepatocyte growth factor / NCAM signaling for neurite out-growth / Regulation of KIT signaling / Role of LAT2/NTAL/LAB on calcium mobilization / cellular response to endothelin / helper T cell diapedesis / cerebellar neuron development / response to cholecystokinin / regulation of leukocyte migration / Downstream signal transduction / regulation of intracellular signal transduction / response to peptide / postsynaptic specialization assembly / Insulin receptor signalling cascade / FCERI mediated MAPK activation / lymphocyte homeostasis / Signal attenuation / NRAGE signals death through JNK / protein phosphorylated amino acid binding / Signaling by SCF-KIT / RAC1 GTPase cycle / regulation of T cell migration / GRB2:SOS provides linkage to MAPK signaling for Integrins / p130Cas linkage to MAPK signaling for integrins / FCERI mediated Ca+2 mobilization / reelin-mediated signaling pathway / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / G alpha (12/13) signalling events / regulation of dendrite development / midbrain morphogenesis / positive regulation of skeletal muscle acetylcholine-gated channel clustering / regulation of pro-B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to yeast / Regulation of signaling by CBL / regulation of Rac protein signal transduction / vitellogenesis / Regulation of actin dynamics for phagocytic cup formation / negative regulation of wound healing / pericardium morphogenesis / cardiac atrium morphogenesis / RET signaling / heart trabecula morphogenesis / negative regulation of cell motility / VEGFA-VEGFR2 Pathway / regulation of T cell differentiation in thymus / protein localization to membrane / GTPase complex / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / blood vessel morphogenesis / cellular response to insulin-like growth factor stimulus / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / establishment of cell polarity / regulation of GTPase activity / enzyme-linked receptor protein signaling pathway / regulation of T cell proliferation / ERBB2-ERBB3 signaling pathway / roof of mouth development / positive regulation of smooth muscle cell migration / dendrite development / eyelid development in camera-type eye / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / B cell homeostasis / hair follicle development / cellular response to nitric oxide / ephrin receptor signaling pathway / regulation of signal transduction Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 1b07.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b07.ent.gz | 16.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/1b07 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b07 | HTTPS FTP |
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-Related structure data
Related structure data | 2semC 3semC 1ckbS 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: 7787.548 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q64010 |
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#2: Protein/peptide | Mass: 1425.657 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: Q62245*PLUS |
#3: Chemical | ChemComp-PYJ / |
#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: 1.93 Å3/Da / Density % sol: 36.31 % | |||||||||||||||
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Crystal grow | pH: 6 Details: 29% PEG4000, 0.2 M AMMONIUM ACETATE, PH 6.0, pH 6.00 | |||||||||||||||
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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 15685 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.062 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 8 % / Rsym value: 0.075 / % possible all: 81.8 |
Reflection | *PLUS Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 81.8 % / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CKB Resolution: 2.5→30 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: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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