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- PDB-6p0i: Crystal structure of GDP-bound human RalA in a covalent complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p0i | ||||||
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Title | Crystal structure of GDP-bound human RalA in a covalent complex with aryl sulfonyl fluoride compounds. | ||||||
![]() | Ras-related protein Ral-A | ||||||
![]() | signaling protein/inhibitor / Ral GTPase / RalA / covalent inhibitor / sulfonyl fluoride / SIGNALING PROTEIN / signaling protein-inhibitor complex | ||||||
Function / homology | ![]() membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / myosin binding ...membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / myosin binding / exocytosis / cleavage furrow / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / synaptic membrane / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / cytoplasmic vesicle membrane / receptor internalization / GDP binding / chemotaxis / ATPase binding / Ras protein signal transduction / cell cycle / cell division / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / cell surface / signal transduction / mitochondrion / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Liu, D. / Ghozayel, M.K. / Xu, D. / Meroueh, S.O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Small-molecule covalent bond formation at tyrosine creates a binding site and inhibits activation of Ral GTPases. Authors: Bum-Erdene, K. / Liu, D. / Gonzalez-Gutierrez, G. / Ghozayel, M.K. / Xu, D. / Meroueh, S.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.2 KB | Display | ![]() |
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PDB format | ![]() | 100.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p0jC ![]() 6p0kC ![]() 6p0lC ![]() 6p0mC ![]() 6p0nC ![]() 6p0oC ![]() 1u8zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 21303.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 204 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NL7.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NL7.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GDP / | ||||
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#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | ChemComp-ACT / | ||||
#5: Chemical | ChemComp-GOL / | ||||
#6: Chemical | ChemComp-NL7 / | ||||
#7: Chemical | ChemComp-CA / | ||||
#8: Chemical | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M Calcium Acetate pH 5.5, 18-22% PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Feb 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→39 Å / Num. obs: 61827 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.048 / Rsym value: 0.045 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.18→1.2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2645 / CC1/2: 0.681 / Rpim(I) all: 0.419 / Rrim(I) all: 0.909 / Rsym value: 0.807 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1u8z Resolution: 1.18→39 Å / SU ML: 0.0808 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→39 Å
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Refine LS restraints |
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LS refinement shell |
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