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- PDB-6wnk: Macrocyclic peptides TDI5575 that selectively inhibit the Mycobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wnk | ||||||
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Title | Macrocyclic peptides TDI5575 that selectively inhibit the Mycobacterium tuberculosis proteasome | ||||||
![]() | (Proteasome subunit ...) x 2 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Mycobacterium tuberculosis / proteasome inhibitor / Macrocyclic peptides / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / modification-dependent protein catabolic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsu, H.C. / Li, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Macrocyclic Peptides that Selectively Inhibit the Mycobacterium tuberculosis Proteasome. Authors: Zhang, H. / Hsu, H.C. / Kahne, S.C. / Hara, R. / Zhan, W. / Jiang, X. / Burns-Huang, K. / Ouellette, T. / Imaeda, T. / Okamoto, R. / Kawasaki, M. / Michino, M. / Wong, T.T. / Toita, A. / ...Authors: Zhang, H. / Hsu, H.C. / Kahne, S.C. / Hara, R. / Zhan, W. / Jiang, X. / Burns-Huang, K. / Ouellette, T. / Imaeda, T. / Okamoto, R. / Kawasaki, M. / Michino, M. / Wong, T.T. / Toita, A. / Yukawa, T. / Moraca, F. / Vendome, J. / Saha, P. / Sato, K. / Aso, K. / Ginn, J. / Meinke, P.T. / Foley, M. / Nathan, C.F. / Darwin, K.H. / Li, H. / Lin, 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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 969.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.7 MB | Display | ![]() |
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Full document | ![]() | 5.8 MB | Display | |
Data in XML | ![]() | 210.7 KB | Display | |
Data in CIF | ![]() | 279.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5trgS S: Starting model for refinement |
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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
-Proteasome subunit ... , 2 types, 28 molecules ABCDEFGOPQRSTUHIJKLMNVWXYZab
#1: Protein | Mass: 25971.975 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5U4D5, proteasome endopeptidase complex #2: Protein | Mass: 25274.264 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5U4D6, proteasome endopeptidase complex |
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-Non-polymers , 4 types, 1212 molecules ![](data/chem/img/U5Y.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/DMF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/DMF.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-U5Y / ( #4: Chemical | ChemComp-CIT / #5: Chemical | ChemComp-DMF / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60mM sodium citrate (pH 6.2), 15% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07812 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→92.97 Å / Num. obs: 332027 / % possible obs: 98.2 % / Redundancy: 7 % / Biso Wilson estimate: 42.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.28→2.4 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 48823 / CC1/2: 0.724 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TRG Resolution: 2.28→87.59 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 53.04 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→87.59 Å
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Refine LS restraints |
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