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Yorodumi- PDB-7oup: Structure of human DPP3 in complex with a hydroxyethylene transit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oup | |||||||||
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Title | Structure of human DPP3 in complex with a hydroxyethylene transition state peptidomimetic | |||||||||
Components |
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Keywords | HYDROLASE / Inhibitor / COMPLEX / PEPTIDASE / ZINC-HYDROLASE | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Kumar, P. / Reithofer, V. / Gruber, K. | |||||||||
Funding support | Austria, 1items
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Citation | Journal: Chemistry / Year: 2021 Title: Efficient Entropy-Driven Inhibition of Dipeptidyl Peptidase III by Hydroxyethylene Transition-State Peptidomimetics. Authors: Ivkovic, J. / Jha, S. / Lembacher-Fadum, C. / Puschnig, J. / Kumar, P. / Reithofer, V. / Gruber, K. / Macheroux, P. / Breinbauer, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oup.cif.gz | 195.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oup.ent.gz | 124.8 KB | Display | PDB format |
PDBx/mmJSON format | 7oup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oup_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 7oup_full_validation.pdf.gz | 451.5 KB | Display | |
Data in XML | 7oup_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 7oup_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/7oup ftp://data.pdbj.org/pub/pdb/validation_reports/ou/7oup | HTTPS FTP |
-Related structure data
Related structure data | 3t6bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AF
#1: Protein | Mass: 82617.875 Da / Num. of mol.: 1 / Mutation: E451A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NY33, dipeptidyl-peptidase III |
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#2: Protein/peptide | (( Mass: 647.803 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: peptide mimetic based on VVFPW with the peptide linkage between V-2 and F-3 replaced by a (S)-hydroxyethylene group Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 76 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-K / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % |
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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, 1.344 M potassium phosphate dibasic monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95373 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2014 / Details: bent collimating mirror and toroid |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→45.3 Å / Num. obs: 23086 / % possible obs: 98.56 % / Redundancy: 3.3 % / Biso Wilson estimate: 53.7 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1165 / Rpim(I) all: 0.075 / Rrim(I) all: 0.1391 / Net I/σ(I): 8.03 |
Reflection shell | Resolution: 2.65→2.75 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7036 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2244 / CC1/2: 0.64 / CC star: 0.884 / Rpim(I) all: 0.4547 / Rrim(I) all: 0.8407 / % possible all: 96.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T6B Resolution: 2.65→45.28 Å / SU ML: 0.4254 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.5819 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 53.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→45.28 Å
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Refine LS restraints |
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LS refinement shell |
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