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Yorodumi- PDB-3w2t: Crystal structure of human depiptidyl peptidase IV (DPP-4) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w2t | ||||||||||||
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Title | Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with vildagliptin | ||||||||||||
Components | Dipeptidyl peptidase 4Dipeptidyl peptidase-4 | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ALPHA/BETA / BETA-PROPELLER / HYDROLASE / AMINOPEPTIDASE / SERINE PROTEASE / SECRETED / SIGNAL-ANCHOR / TRANSMEMBRANE / DIABETES / GLYCOPROTEIN / CELL MEMBRANE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / 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 / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / 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) / virus receptor activity / lamellipodium / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||||||||
Authors | Kishida, H. / Nabeno, M. / Miyaguchi, I. / Tanaka, Y. / Katou, R. / Akahoshi, F. | ||||||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: A comparative study of the binding modes of recently launched dipeptidyl peptidase IV inhibitors in the active site Authors: Nabeno, M. / Akahoshi, F. / Kishida, H. / Miyaguchi, I. / Tanaka, Y. / Ishii, S. / Kadowaki, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w2t.cif.gz | 334 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w2t.ent.gz | 268.6 KB | Display | PDB format |
PDBx/mmJSON format | 3w2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/3w2t ftp://data.pdbj.org/pub/pdb/validation_reports/w2/3w2t | HTTPS FTP |
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-Related structure data
Related structure data | 3vjmS 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 85880.031 Da / Num. of mol.: 2 / Fragment: UNP residues 33-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Plasmid: pPSC8 / Cell line (production host): expresSF+ / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV |
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-Sugars , 3 types, 13 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 1031 molecules
#4: Chemical | #5: Chemical | #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: 2.98 Å3/Da / Density % sol: 58.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 20% PEG 4000, 0.18M sodium acetate, 0.18M glycine-sodium hydroxide, pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→50 Å / Num. all: 84864 / Num. obs: 82418 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.36→2.44 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 6.96 / Num. unique all: 7691 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VJM Resolution: 2.36→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.142 / SU ML: 0.148 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.872 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.362→2.423 Å / Total num. of bins used: 20
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