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Yorodumi- PDB-1orw: Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1orw | |||||||||
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Title | Crystal Structure of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with a Peptidomimetic Inhibitor | |||||||||
Components | dipeptidyl peptidase IV | |||||||||
Keywords | HYDROLASE / serine protease / oxyanion hole / substrate channeling / drug design / diabetes mellitus | |||||||||
Function / homology | Function and homology information Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / anchoring junction / lamellipodium membrane / endocytic vesicle / endothelial cell migration / aminopeptidase activity ...Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / anchoring junction / lamellipodium membrane / endocytic vesicle / endothelial cell migration / aminopeptidase activity / T cell costimulation / lamellipodium / protease binding / cell adhesion / apical plasma membrane / membrane raft / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | |||||||||
Authors | Engel, M. / Hoffmann, T. / Wagner, L. / Wermann, M. / Heiser, U. / Kiefersauer, R. / Huber, R. / Bode, W. / Demuth, H.U. / Brandstetter, H. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: The Crystal Structure of Dipeptidyl Peptidase IV (CD26) Reveals its Functional Regulation and Enzymatic Mechanism Authors: Engel, M. / Hoffmann, T. / Wagner, L. / Wermann, M. / Heiser, U. / Kiefersauer, R. / Huber, R. / Bode, W. / Demuth, H.U. / Brandstetter, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1orw.cif.gz | 609.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1orw.ent.gz | 506.7 KB | Display | PDB format |
PDBx/mmJSON format | 1orw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1orw ftp://data.pdbj.org/pub/pdb/validation_reports/or/1orw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 84429.281 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAIN / Source method: isolated from a natural source / Details: kidney / Source: (natural) Sus scrofa (pig) References: GenBank: 28566188, UniProt: P22411*PLUS, dipeptidyl-peptidase IV |
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-Sugars , 3 types, 24 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 830 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-PHI / #7: Chemical | ChemComp-P2Y / ( #8: Water | ChemComp-HOH / | |
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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: 2.53 Å3/Da / Density % sol: 50.99 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 2000, 0.1 M ammonium sulfate, 0.1 M Tris/HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.4 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 12, 2000 / Details: undulator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→29.78 Å / Num. all: 157559 / Num. obs: 157559 / Biso Wilson estimate: 34.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→29.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2736894.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.6655 Å2 / ksol: 0.352201 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
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Refine analyze | Luzzati coordinate error free: 0.38 Å / Luzzati sigma a free: 0.48 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→29.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.84→3.02 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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