[English] 日本語
![](img/lk-miru.gif)
- PDB-2gs6: Crystal Structure of the active EGFR kinase domain in complex wit... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2gs6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the active EGFR kinase domain in complex with an ATP analog-peptide conjugate | ||||||
![]() |
| ||||||
![]() | TRANSFERASE / EGFR / kinase / active / ATP-analog peptide conjugate | ||||||
Function / homology | ![]() : / : / : / positive regulation of miRNA processing / cellular response to xenobiotic stimulus => GO:0071466 / negative regulation of ERBB signaling pathway / magnesium ion homeostasis / regulation of nitric-oxide synthase activity / ERBB2 signaling pathway / multicellular organism development ...: / : / : / positive regulation of miRNA processing / cellular response to xenobiotic stimulus => GO:0071466 / negative regulation of ERBB signaling pathway / magnesium ion homeostasis / regulation of nitric-oxide synthase activity / ERBB2 signaling pathway / multicellular organism development / clathrin-coated vesicle membrane / membrane organization / regulation of cell motility / positive regulation of kinase activity / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to osmotic stress / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / positive regulation of nitric oxide mediated signal transduction / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of Notch signaling pathway / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / plasma membrane => GO:0005886 / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / endocytic vesicle / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cell surface receptor protein tyrosine kinase signaling pathway / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / cellular response to cadmium ion / positive regulation of DNA repair / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / ossification / cellular response to dexamethasone stimulus / basal plasma membrane / neurogenesis / regulation of ERK1 and ERK2 cascade / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of epithelial cell proliferation / astrocyte activation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Gureasko, J. / Shen, K. / Cole, P.A. / Kuriyan, J. | ||||||
![]() | ![]() Title: An Allosteric Mechanism for Activation of the Kinase Domain of Epidermal Growth Factor Receptor Authors: Zhang, X. / Gureasko, J. / Shen, K. / Cole, P.A. / Kuriyan, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 704.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 711.6 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gs2C ![]() 2gs7C ![]() 1m14S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is an asymmetric dimer that is generated by a 3(2) fold operation of the monomer in the asymmetric unit: -z+3/2,x-1/2,-y+1/2 |
-
Components
#1: Protein | Mass: 37563.457 Da / Num. of mol.: 1 / Fragment: kinase domain, residues 696-1022 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H2C9, UniProt: P00533*PLUS, receptor protein-tyrosine kinase |
---|---|
#2: Protein/peptide | Mass: 1544.657 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-112 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 18% PEG3350, 0.2 M LiCitrate, 4% Polypropropylene Glycol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2004 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 15419 / Num. obs: 15419 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rsym value: 0.147 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.6→2.7 Å / Mean I/σ(I) obs: 5.6 / Rsym value: 0.46 / % possible all: 96.5 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1M14 Resolution: 2.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Bsol: 41.326 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.087 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Xplor file |
|