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Yorodumi- PDB-1tkr: Human Dipeptidyl Peptidase IV/CD26 inhibited with Diisopropyl Flu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tkr | |||||||||
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Title | Human Dipeptidyl Peptidase IV/CD26 inhibited with Diisopropyl FluoroPhosphate | |||||||||
Components | Dipeptidyl peptidase IV | |||||||||
Keywords | HYDROLASE / alpha/beta Hydrolase / beta-Propeller / Homodimer | |||||||||
Function / homology | Function and homology information glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / cell adhesion / response to hypoxia / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / signaling receptor binding / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Bjelke, J.R. / Christensen, J. / Branner, S. / Wagtmann, N. / Olsen, C. / Kanstrup, A.B. / Rasmussen, H.B. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Tyrosine 547 Constitutes an Essential Part of the Catalytic Mechanism of Dipeptidyl Peptidase IV Authors: Bjelke, J.R. / Christensen, J. / Branner, S. / Wagtmann, N. / Olsen, C. / Kanstrup, A.B. / Rasmussen, H.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tkr.cif.gz | 326.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tkr.ent.gz | 264.8 KB | Display | PDB format |
PDBx/mmJSON format | 1tkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tkr_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 1tkr_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 1tkr_validation.xml.gz | 65.1 KB | Display | |
Data in CIF | 1tkr_validation.cif.gz | 92.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/1tkr ftp://data.pdbj.org/pub/pdb/validation_reports/tk/1tkr | HTTPS FTP |
-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, 2 molecules AB
#1: Protein | Mass: 84462.617 Da / Num. of mol.: 2 / Fragment: Extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Plasmid: pBlueBAC4.5 / Cell line (production host): High5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV |
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-Sugars , 8 types, 12 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||||
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||||
#4: 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 #5: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #10: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 695 molecules
#9: Chemical | #11: 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: 2.8 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, Sodium acetate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30.6 Å / Num. obs: 49786 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 51.4 Å2 |
Reflection shell | Resolution: 2.7→2.87 Å / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30.6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 318716.25 / 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: 50.2276 Å2 / ksol: 0.425547 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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