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- PDB-7p70: The PDZ-domain of SNTB1 complexed with the PDZ-binding motif of H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p70 | ||||||
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Title | The PDZ-domain of SNTB1 complexed with the PDZ-binding motif of HPV35-E6 | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gogl, G. / Cousido-Siah, A. / Trave, G. | ||||||
![]() | ![]() Title: Quantitative fragmentomics allow affinity mapping of interactomes. Authors: Gogl, G. / Zambo, B. / Kostmann, C. / Cousido-Siah, A. / Morlet, B. / Durbesson, F. / Negroni, L. / Eberling, P. / Jane, P. / Nomine, Y. / Zeke, A. / Ostergaard, S. / Monsellier, E. / Vincentelli, R. / Trave, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.8 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7p71C ![]() 7p72C ![]() 7p73C ![]() 7p74C ![]() 2vrfS ![]() 5n7dS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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/peptide | Mass: 1536.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-terminal biotin-ttds label / Source: (synth.) ![]() ![]() | ||||||
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#2: Protein | Mass: 46699.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% polyethylene glycol 3350, 200 mM sodium malonate buffered at pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→46 Å / Num. obs: 32358 / % possible obs: 99.5 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rrim(I) all: 0.153 / Net I/σ(I): 12.57 |
Reflection shell | Resolution: 2→2.05 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 2327 / CC1/2: 0.503 / Rrim(I) all: 2.13 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5N7D, 2VRF Resolution: 2→45.897 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.63 Å2 / Biso mean: 46.0567 Å2 / Biso min: 17.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→45.897 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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