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- PDB-5e3a: Structure of human DPP3 in complex with opioid peptide leu-enkephalin -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e3a | ||||||||||||
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Title | Structure of human DPP3 in complex with opioid peptide leu-enkephalin | ||||||||||||
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![]() | HYDROLASE / Peptide-complex / Zinc-hydrolase / opioid-peptide / peptidase | ||||||||||||
Function / homology | ![]() synaptic vesicle lumen / neuronal dense core vesicle lumen / dipeptidyl-peptidase III / chromaffin granule lumen / opioid receptor binding / opioid peptide activity / synaptic signaling via neuropeptide / general adaptation syndrome, behavioral process / aggressive behavior / positive regulation of behavioral fear response ...synaptic vesicle lumen / neuronal dense core vesicle lumen / dipeptidyl-peptidase III / chromaffin granule lumen / opioid receptor binding / opioid peptide activity / synaptic signaling via neuropeptide / general adaptation syndrome, behavioral process / aggressive behavior / positive regulation of behavioral fear response / symmetric synapse / G protein-coupled opioid receptor signaling pathway / response to epinephrine / cell body fiber / sensory perception / cellular response to vitamin D / neuropeptide hormone activity / metalloexopeptidase activity / dipeptidyl-peptidase activity / startle response / transmission of nerve impulse / locomotory exploration behavior / response to immobilization stress / behavioral fear response / neuropeptide signaling pathway / glial cell proliferation / aminopeptidase activity / axon terminus / cellular response to cAMP / sensory perception of pain / cellular response to transforming growth factor beta stimulus / Peptide ligand-binding receptors / Post-translational protein phosphorylation / response to nicotine / protein catabolic process / response to toxic substance / cellular response to virus / response to calcium ion / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / KEAP1-NFE2L2 pathway / response to estradiol / Neddylation / cellular response to oxidative stress / G alpha (i) signalling events / chemical synaptic transmission / perikaryon / response to ethanol / response to lipopolysaccharide / response to hypoxia / endoplasmic reticulum lumen / neuronal cell body / dendrite / signal transduction / proteolysis / zinc ion binding / extracellular exosome / extracellular region / plasma membrane / 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 | ![]() | 166.8 KB | Display | ![]() |
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PDB format | ![]() | 129.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.9 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e2qC ![]() 5e33C ![]() 5e3cC ![]() 5egyC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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: Protein/peptide | Mass: 555.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: opioid peptide from human source / Source: (synth.) ![]() |
-Non-polymers , 4 types, 367 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
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![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.056M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 1.344M POTASSIUM PHOSPHATE DIBASIC 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: Apr 20, 2015 |
Radiation | Monochromator: liquid nitrogen cooled channel-cut silicon monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→39.58 Å / Num. all: 48267 / Num. obs: 48267 / % possible obs: 95.09 % / Redundancy: 3 % / Biso Wilson estimate: 32.96 Å2 / Rmerge(I) obs: 0.08875 / Rsym value: 0.08875 / Net I/σ(I): 10.73 |
Reflection shell | Resolution: 2.05→2.121 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6197 / Mean I/σ(I) obs: 1.85 / % possible all: 95.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3T6B Resolution: 2.05→39.576 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / ESU R: 0.2088 / ESU R Free: 0.259 / Phase error: 30.47 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→39.576 Å
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Refine LS restraints |
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LS refinement shell |
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