+Open data
-Basic information
Entry | Database: PDB / ID: 3o9v | |||||||||
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Title | Crystal Structure of Human DPP4 Bound to TAK-986 | |||||||||
Components | Dipeptidyl peptidase 4 | |||||||||
Keywords | HYDROLASE / SIGNALING PROTEIN/INHIBITOR / protease and 8-bladed beta-propeller domain / Aminopeptidase / Cell membrane / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å | |||||||||
Authors | Yano, J.K. / Aertgeerts, K. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Discovery of a 3-Pyridylacetic Acid Derivative (TAK-100) as a Potent, Selective and Orally Active Dipeptidyl Peptidase IV (DPP-4) Inhibitor. Authors: Miyamoto, Y. / Banno, Y. / Yamashita, T. / Fujimoto, T. / Oi, S. / Moritoh, Y. / Asakawa, T. / Kataoka, O. / Yashiro, H. / Takeuchi, K. / Suzuki, N. / Ikedo, K. / Kosaka, T. / Tsubotani, S. ...Authors: Miyamoto, Y. / Banno, Y. / Yamashita, T. / Fujimoto, T. / Oi, S. / Moritoh, Y. / Asakawa, T. / Kataoka, O. / Yashiro, H. / Takeuchi, K. / Suzuki, N. / Ikedo, K. / Kosaka, T. / Tsubotani, S. / Tani, A. / Sasaki, M. / Funami, M. / Amano, M. / Yamamoto, Y. / Aertgeerts, K. / Yano, J. / Maezaki, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o9v.cif.gz | 591.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o9v.ent.gz | 486.6 KB | Display | PDB format |
PDBx/mmJSON format | 3o9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o9v_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 3o9v_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 3o9v_validation.xml.gz | 60.5 KB | Display | |
Data in CIF | 3o9v_validation.cif.gz | 92.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/3o9v ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9v | HTTPS FTP |
-Related structure data
Related structure data | 3o95C 1r9mS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 85775.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADCP2, CD26, DPP4 / Plasmid: pFASTBAC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV #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: Chemical | ChemComp-10T / #4: Sugar | ChemComp-NAG / #5: 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: 2.88 Å3/Da / Density % sol: 57.33 % |
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Crystal grow | Temperature: 277 K / Method: sitting drop, vapor diffusion Details: 20% PEG MME 2000, 100 mM Bicine, pH 8-8.5, sitting drop, vapor diffusion, temperature 277K PH range: 8-8.5 |
-Data collection
Diffraction | Mean temperature: 92 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.75→50 Å / Num. all: 101631 / Num. obs: 100525 / % possible obs: 98.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1R9M Resolution: 2.75→35 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / SU B: 27.288 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.346 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.745→2.816 Å / Total num. of bins used: 20
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