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Open data
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Basic information
Entry | Database: PDB / ID: 5egy | |||||||||
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Title | Structure of ligand free human DPP3 in closed form. | |||||||||
![]() | Dipeptidyl peptidase 3 | |||||||||
![]() | HYDROLASE / Unbound / Peptidase / Zinc | |||||||||
Function / homology | ![]() dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / protein catabolic process / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / zinc ion binding / extracellular exosome ...dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / protein catabolic process / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / zinc ion binding / extracellular exosome / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kumar, P. / Reithofer, V. / Reisinger, M. / Pavkov-Keller, T. / Wallner, S. / Macheroux, P. / Gruber, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition. Authors: Kumar, P. / Reithofer, V. / Reisinger, M. / Wallner, S. / Pavkov-Keller, T. / Macheroux, P. / Gruber, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.6 KB | Display | ![]() |
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PDB format | ![]() | 121.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.7 KB | Display | ![]() |
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Full document | ![]() | 435.5 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e2qC ![]() 5e33C ![]() 5e3aC ![]() 5e3cC ![]() 5ehhC ![]() 3t6bS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 81548.688 Da / Num. of mol.: 1 / Mutation: C19S, E207C, E451A, S491C, C519S, C654S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH- 8.2, 293K PH range: 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→48.83 Å / Num. all: 20281 / Num. obs: 20281 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 69.01 Å2 / Rmerge(I) obs: 0.0723 / Rsym value: 0.0723 / Net I/σ(I): 12.01 |
Reflection shell | Resolution: 2.74→2.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7944 / Mean I/σ(I) obs: 1.64 / % possible all: 96.02 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3T6B Resolution: 2.741→43.83 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.741→43.83 Å
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Refine LS restraints |
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LS refinement shell |
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