+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+33 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human DPP3 in complex with met-enkephalin | ||||||||||||
Components |
| ||||||||||||
Keywords | HYDROLASE / Complex / Opioid-peptide / Zinc-hydrolase / peptidase | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.837 Å | ||||||||||||
Authors | Kumar, P. / Reithofer, V. / Reisinger, M. / Pavkov-Keller, T. / Wallner, S. / Macheroux, P. / Gruber, K. | ||||||||||||
Funding support | Austria, 1items
| ||||||||||||
Citation | Journal: Sci Rep / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5e33.cif.gz | 172 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5e33.ent.gz | 133.7 KB | Display | PDB format |
PDBx/mmJSON format | 5e33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e33_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5e33_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 5e33_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 5e33_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/5e33 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/5e33 | HTTPS FTP |
-Related structure data
Related structure data | 5e2qC 5e3aC 5e3cC 5egyC 5ehhC 3t6bS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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.) Homo sapiens (human) / Gene: DPP3 / Plasmid: PET28MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NY33, dipeptidyl-peptidase III |
---|---|
#2: Protein/peptide | Mass: 573.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01210*PLUS |
-Non-polymers , 4 types, 523 molecules
#3: Chemical | ChemComp-ZN / | ||||
---|---|---|---|---|---|
#4: Chemical | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phospahte dibasic, pH- 8.2 PH range: 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å |
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: 1.83→45.42 Å / Num. all: 68276 / Num. obs: 68276 / % possible obs: 96.86 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.13 Å2 / Rmerge(I) obs: 0.05052 / Rsym value: 0.05052 / Net I/σ(I): 14.78 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.75 / % possible all: 93.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T6B Resolution: 1.837→45.416 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.35 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.837→45.416 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|