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- PDB-4jmo: Complexe of ARNO Sec7 domain with the protein-protein interaction... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jmo | ||||||
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Title | Complexe of ARNO Sec7 domain with the protein-protein interaction inhibitor N-(4-hydroxy-2,6-dimethylphenyl)-4-methoxybenzenesulfonamide | ||||||
![]() | Cytohesin-2 | ||||||
![]() | SIGNALING PROTEIN/INHIBITOR / Nucleotide exchange factor / ARF1 / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane ...Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / bicellular tight junction / guanyl-nucleotide exchange factor activity / adherens junction / endocytosis / growth cone / actin cytoskeleton organization / Golgi membrane / lipid binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoh, F. / Rouhana, J. | ||||||
![]() | ![]() Title: Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors Authors: Rouhana, J. / Hoh, F. / Estaran, S. / Henriquet, C. / Boublik, Y. / Kerkour, A. / Trouillard, R. / Martinez, J. / Pugniere, M. / Padilla, A. / Chavanieu, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.7 KB | Display | ![]() |
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PDB format | ![]() | 77.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.6 KB | Display | ![]() |
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Full document | ![]() | 759.2 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jmiSC ![]() 4jwlC ![]() 4jxhC ![]() 4l5mC 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
#1: Protein | Mass: 23029.312 Da / Num. of mol.: 1 / Fragment: Sec7 domain, UNP residues 56-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-JAF / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M MgSO4,Peg5K MME 18%, 0.1M Tris-HCl, pH 8.5 , VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40.22 Å / Num. obs: 22395 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.321 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JMI Resolution: 1.8→40.22 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.335 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 3.5 / ESU R: 0.162 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.883 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.849 Å / Total num. of bins used: 20
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