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- PDB-7ayr: Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ayr | ||||||
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Title | Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B115 | ||||||
![]() | Dipeptidyl peptidase 8 | ||||||
![]() | HYDROLASE / DPP8 / Protease | ||||||
Function / homology | ![]() dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / aminopeptidase activity / serine-type peptidase activity / immune response / apoptotic process / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ross, B.H. / Huber, R. | ||||||
![]() | ![]() Title: Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9. Authors: Carvalho, L.A.R. / Ross, B. / Fehr, L. / Bolgi, O. / Wohrle, S. / Lum, K.M. / Podlesainski, D. / Vieira, A.C. / Kiefersauer, R. / Felix, R. / Rodrigues, T. / Lucas, S.D. / Gross, O. / Geiss- ...Authors: Carvalho, L.A.R. / Ross, B. / Fehr, L. / Bolgi, O. / Wohrle, S. / Lum, K.M. / Podlesainski, D. / Vieira, A.C. / Kiefersauer, R. / Felix, R. / Rodrigues, T. / Lucas, S.D. / Gross, O. / Geiss-Friedlander, R. / Cravatt, B.F. / Huber, R. / Kaiser, M. / Moreira, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337.1 KB | Display | ![]() |
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PDB format | ![]() | 269.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 976.2 KB | Display | ![]() |
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Full document | ![]() | 994.2 KB | Display | |
Data in XML | ![]() | 54.8 KB | Display | |
Data in CIF | ![]() | 74.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a3gC ![]() 7a3jC ![]() 7a3lC ![]() 7ayqC ![]() 7or4C ![]() 7oz7C ![]() 7zxsC ![]() 6eooS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 103483.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.46 mM Na citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.69→48.96 Å / Num. obs: 94352 / % possible obs: 100 % / Redundancy: 13.127 % / Biso Wilson estimate: 78.248 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.065 / Χ2: 0.899 / Net I/σ(I): 28.62 / Num. measured all: 1238539 / Scaling rejects: 101 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EOO Resolution: 2.69→48.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.694 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 196.28 Å2 / Biso mean: 77.522 Å2 / Biso min: 41.76 Å2
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Refinement step | Cycle: final / Resolution: 2.69→48.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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