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- PDB-4jxh: 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: 4jxh | ||||||
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Title | Complexe of ARNO Sec7 domain with the protein-protein interaction inhibitor N-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide at pH 8.5 | ||||||
![]() | Cytohesin-2 | ||||||
![]() | SIGNALING PROTEIN/INHIBITOR / sec 7 domain / 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 | ![]() | 107.8 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.5 KB | Display | ![]() |
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Full document | ![]() | 807.6 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jmiSC ![]() 4jmoC ![]() 4jwlC ![]() 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: 24918.410 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-HRC / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M MgSO4, 18% PEG 5000 MME, 0.1M TRIS- HCL, PH 8.5, VAPOR DIFFUSION, HANGING 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: May 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→36.55 Å / Num. all: 40862 / Num. obs: 38676 / % possible obs: 99.67 % |
Reflection shell | Resolution: 1.469→1.508 Å / % possible all: 99.7 |
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Processing
Software | Name: REFMAC / Version: 5.7.0032 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4JMI Resolution: 1.47→36.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.52 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / 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: 19.591 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→36.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.469→1.508 Å / Total num. of bins used: 20
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