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- PDB-7ayq: 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: 7ayq | ||||||
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Title | Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B114 | ||||||
![]() | Dipeptidyl peptidase 8 | ||||||
![]() | HYDROLASE / DPP8 / Peptidase / 4-oxo-b-lactamic | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ross, B. / 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 | ![]() | 344.5 KB | Display | ![]() |
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PDB format | ![]() | 275.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7a3gC ![]() 7a3jC ![]() 7a3lC ![]() 7ayrC ![]() 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 103483.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 173 molecules ![](data/chem/img/TMO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/S9Z.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/S9Z.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #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: 4.2 Å3/Da / Density % sol: 70.7 % |
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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: 2.45→48.94 Å / Num. obs: 124546 / % possible obs: 100 % / Redundancy: 13.161 % / Biso Wilson estimate: 69.989 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.072 / Χ2: 0.893 / Net I/σ(I): 23.16 / Num. measured all: 1639145 / Scaling rejects: 62 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EOO Resolution: 2.45→48.94 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.829 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.191 / 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: 181.85 Å2 / Biso mean: 65.657 Å2 / Biso min: 39.01 Å2
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Refinement step | Cycle: final / Resolution: 2.45→48.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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