[English] 日本語
![](img/lk-miru.gif)
- PDB-8d1t: Crystal structure of human USP30 in complex with a covalent inhib... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8d1t | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human USP30 in complex with a covalent inhibitor 552 and a Fab | |||||||||
![]() |
| |||||||||
![]() | 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
| |||||||||
![]() | ![]() Title: TBD Authors: Song, X. / Butler, J. / Li, C. / Zhang, K. / Zhang, D. / Hao, Y. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 160.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 120.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 804.2 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m43S ![]() 5ohkS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() |
---|
-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.) ![]() ![]() ![]() |
---|---|
#3: Antibody | Mass: 23653.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 33 molecules ![](data/chem/img/PXW.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PXW / ( |
---|---|
#5: Chemical | ChemComp-ZN / |
#6: Chemical | ChemComp-EDO / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8.5, 22% PEG 4000, 4% 1,3-Butanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 2.94→41.78 Å / Num. obs: 18857 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 79.39 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.94→3.12 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2985 / % possible all: 98.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5OHK, 4M43 Resolution: 2.94→40.7 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.22 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.41 Å2 / Biso mean: 92.9642 Å2 / Biso min: 24.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.94→40.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
|