[English] 日本語
![](img/lk-miru.gif)
- PDB-7juy: Crystal Structure of KSR1:MEK1 in complex with AMP-PNP, and allos... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7juy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of KSR1:MEK1 in complex with AMP-PNP, and allosteric MEK inhibitor Cobimetinib | |||||||||
![]() |
| |||||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Pseudokinase / drug target / cell signaling and cancer / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | ![]() regulation of MAP kinase activity / mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / regulation of Golgi inheritance / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / MAP kinase kinase activity / 14-3-3 protein binding / cAMP-mediated signaling / RAF activation ...regulation of MAP kinase activity / mitogen-activated protein kinase kinase / MAP-kinase scaffold activity / regulation of Golgi inheritance / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / MAP kinase kinase activity / 14-3-3 protein binding / cAMP-mediated signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / ruffle membrane / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / late endosome / regulation of cell population proliferation / protein tyrosine kinase activity / Ras protein signal transduction / positive regulation of MAPK cascade / early endosome / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / centrosome / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Khan, Z.M. / Dar, A.C. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural basis for the action of the drug trametinib at KSR-bound MEK. Authors: Khan, Z.M. / Real, A.M. / Marsiglia, W.M. / Chow, A. / Duffy, M.E. / Yerabolu, J.R. / Scopton, A.P. / Dar, A.C. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 140.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 104.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7juqC ![]() 7jurC ![]() 7jusC ![]() 7jutC ![]() 7juuC ![]() 7juvC ![]() 7juwC ![]() 7juxC ![]() 7juzC ![]() 7jv0C ![]() 7jv1C ![]() 2y4iS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 2 molecules BC
#1: Protein | Mass: 38597.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8IVT5, non-specific serine/threonine protein kinase |
---|---|
#2: Protein | Mass: 43119.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P29678, mitogen-activated protein kinase kinase |
-Non-polymers , 4 types, 6 molecules ![](data/chem/img/ANP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EUI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EUI.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EUI / [ | #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | The author states that kinase suppressor of Ras 1 chain B is proteolytically cleaved between Trp632 ...The author states that kinase suppressor of Ras 1 chain B is proteolytically cleaved between Trp632 and His633. |
---|---|
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.62 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 2000, MES, pH 6.5, Magnesium acetate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.096→49.648 Å / Num. obs: 22409 / % possible obs: 99.9 % / Redundancy: 11.95 % / CC1/2: 1 / Net I/σ(I): 20.04 |
Reflection shell | Resolution: 3.1→3.18 Å / Num. unique obs: 1608 / CC1/2: 0.519 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2Y4I Resolution: 3.096→49.648 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.17 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.096→49.648 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|