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- PDB-7xqv: The complex of nanobody Rh57 binding to GTP-bound RhoA active form -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xqv | |||||||||
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Title | The complex of nanobody Rh57 binding to GTP-bound RhoA active form | |||||||||
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![]() | PROTEIN BINDING | |||||||||
Function / homology | ALANINE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, Y.R. / Liu, R. / Ding, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the binding of nanobody Rh57 to active RhoA-GTP. Authors: Zhang, Y. / Cheng, S. / Zhong, P. / Wang, Z. / Liu, R. / Ding, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.5 KB | Display | ![]() |
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PDB format | ![]() | 51.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.3 KB | Display | ![]() |
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Full document | ![]() | 781.3 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kmqS S: Starting model for refinement |
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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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1 |
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Unit cell |
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Components
-Protein / Antibody , 2 types, 2 molecules AB
#1: Protein | Mass: 20696.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 16209.780 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 7 molecules ![](data/chem/img/ALA.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ALA / |
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#4: Chemical | ChemComp-GNP / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 8000; 100 mM Tris base/ Hydrochloric acid, pH 8.5; 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Oct 6, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→71.01 Å / Num. obs: 9414 / % possible obs: 99.9 % / Redundancy: 25.3 % / Biso Wilson estimate: 75.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.381 / Rpim(I) all: 0.077 / Rrim(I) all: 0.389 / Net I/σ(I): 14.9 / Num. measured all: 237878 / Scaling rejects: 2202 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KMQ Resolution: 2.76→62.25 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.59 Å2 / Biso mean: 78.0749 Å2 / Biso min: 40.33 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.76→62.25 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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