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- PDB-8d0a: Crystal structure of human USP30 in complex with a covalent inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d0a | |||||||||
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Title | Crystal structure of human USP30 in complex with a covalent inhibitor 829 and a Fab | |||||||||
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![]() | HYDROLASE / deubiquitinase / covalent inhibitor | |||||||||
Function / homology | ![]() protein K6-linked deubiquitination / protein K11-linked deubiquitination / pexophagy / autophagy of mitochondrion / deubiquitinase activity / negative regulation of mitophagy / peroxisomal membrane / mitochondrial fusion / protein deubiquitination / Pexophagy ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / pexophagy / autophagy of mitochondrion / deubiquitinase activity / negative regulation of mitophagy / peroxisomal membrane / mitochondrial fusion / protein deubiquitination / Pexophagy / mitochondrial outer membrane / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Song, X. / Butler, J. / Li, C. / Zhang, K. / Zhang, D. / Hao, Y. | |||||||||
Funding support | 2items
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![]() | ![]() Title: TBD Authors: Song, X. / Butler, J. / Hao, 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 | ![]() | 155.9 KB | Display | ![]() |
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PDB format | ![]() | 118.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739.7 KB | Display | ![]() |
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Full document | ![]() | 745 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m43S ![]() 5ohkS 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 , 1 types, 1 molecules A
#1: Protein | Mass: 40159.344 Da / Num. of mol.: 1 / Mutation: F348D,M350S,I353E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 23822.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Antibody | Mass: 23653.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 21 molecules ![](data/chem/img/PKH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PKH / ~{ |
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#5: Chemical | ChemComp-ZN / |
#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: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 22% PEG 4000, 4% 2,2,2-Trifluoroethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 3.19→42.11 Å / Num. obs: 14848 / % possible obs: 98.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.19→3.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2656 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OHK, 4M43 Resolution: 3.19→42.11 Å / Extinction coef esd: 0.9881 / Cross valid method: THROUGHOUT / σ(F): 1.34
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Refinement step | Cycle: LAST / Resolution: 3.19→42.11 Å
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LS refinement shell |
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