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Yorodumi- PDB-3t6j: Structure of human DPPIII in complex with the opioid peptide Tyno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t6j | ||||||
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Title | Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 3.0 Angstroms | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / human dipeptidylpeptidase III / entropy binding / opioid peptide complex / domain motion / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / protein catabolic process / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / extracellular exosome / zinc ion binding ...dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / protein catabolic process / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / extracellular exosome / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.976 Å | ||||||
Authors | Bezerra, G.A. / Gruber, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III. Authors: Bezerra, G.A. / Dobrovetsky, E. / Viertlmayr, R. / Dong, A. / Binter, A. / Abramic, M. / Macheroux, P. / Dhe-Paganon, S. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t6j.cif.gz | 140.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t6j.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 3t6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t6j ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t6j | HTTPS FTP |
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-Related structure data
Related structure data | 3fvySC 3t6bC C: citing same article (ref.) 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
#1: Protein | Mass: 81606.789 Da / Num. of mol.: 1 / Mutation: E451A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP3, hDPPIII / Plasmid: pET28MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NY33, dipeptidyl-peptidase III |
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#2: Protein/peptide | Mass: 662.775 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: truncated version of a human opioid peptide, Spinorphin Source: (synth.) Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
Compound details | synthetic opioid peptide |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.29 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.2 Details: 0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.4 % / Av σ(I) over netI: 4.8 / Number: 39160 / Rsym value: 0.06 / D res high: 2.973 Å / D res low: 79.907 Å / Num. obs: 16399 / % possible obs: 96.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.973→79.907 Å / Num. all: 16399 / Num. obs: 16399 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Rsym value: 0.06 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 42.98 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FVY Resolution: 2.976→19.6 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7967 / SU ML: 0.34 / σ(F): 1.33 / Phase error: 27.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.914 Å2 / ksol: 0.299 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 259.39 Å2 / Biso mean: 68.9701 Å2 / Biso min: 7.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.976→19.6 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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