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Yorodumi- PDB-2ajb: Porcine dipeptidyl peptidase IV (CD26) in complex with the tripep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ajb | |||||||||
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Title | Porcine dipeptidyl peptidase IV (CD26) in complex with the tripeptide tert-butyl-Gly-L-Pro-L-Ile (tBu-GPI) | |||||||||
Components | Dipeptidyl peptidase 4Dipeptidyl peptidase-4 | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Serine protease / dipeptidyl peptidase / alpha/beta-hydrolase / beta-propeller / oxyanion hole / substrate channeling / drug design / diabetes mellitus / flexibility / hydrolase-hydrolase inhibitor complex | |||||||||
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 neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase 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 neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / virus receptor activity / lamellipodium / protease binding / response to hypoxia / cell adhesion / membrane raft / apical plasma membrane / signaling receptor binding / serine-type endopeptidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Engel, M. / Hoffmann, T. / Manhart, S. / Heiser, U. / Chambre, S. / Huber, R. / Demuth, H.U. / Bode, W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Rigidity and flexibility of dipeptidyl peptidase IV: crystal structures of and docking experiments with DPIV. Authors: Engel, M. / Hoffmann, T. / Manhart, S. / Heiser, U. / Chambre, S. / Huber, R. / Demuth, H.U. / Bode, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ajb.cif.gz | 621.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ajb.ent.gz | 507.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ajb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/2ajb ftp://data.pdbj.org/pub/pdb/validation_reports/aj/2ajb | HTTPS FTP |
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-Related structure data
Related structure data | 2aj8C 2ajcC 2ajdC 1orvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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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 / Source: (natural) Sus scrofa (pig) / Organ: Kidney / References: UniProt: P22411, 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 #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 850 molecules
#4: Chemical | ChemComp-0QG / #6: Chemical | ChemComp-SO4 / #7: 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: 2.48 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 2000, 0.1 M AMMONIUM SULFATE, 0.1 M TRIS/HCL PH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→20 Å / Num. obs: 87140 / % possible obs: 92.9 % / Rmerge(I) obs: 0.073 / Χ2: 1.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ORV Resolution: 2.75→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2706631 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.145 Å2 / ksol: 0.321 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→19.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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