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Yorodumi- PDB-4pnz: Human dipeptidyl peptidase IV/CD26 in complex with the long-actin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pnz | |||||||||
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Title | Human dipeptidyl peptidase IV/CD26 in complex with the long-acting inhibitor Omarigliptin (MK-3102) | |||||||||
Components | Dipeptidyl peptidase 4Dipeptidyl peptidase-4 | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / alpha/beta / beta-propeller / dimer / diabetes / aminopeptidase / cell membrane / disulfide bond / glycoprotein / secreted / serine protease / signal-anchor / transmembrane / 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 / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / 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 / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / serine-type peptidase activity / T cell activation / 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 / FOURIER SYNTHESIS / Resolution: 1.9 Å | |||||||||
Authors | Scapin, G. / Yan, Y. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Omarigliptin (MK-3102): A Novel Long-Acting DPP-4 Inhibitor for Once-Weekly Treatment of Type 2 Diabetes. Authors: Biftu, T. / Sinha-Roy, R. / Chen, P. / Qian, X. / Feng, D. / Kuethe, J.T. / Scapin, G. / Gao, Y.D. / Yan, Y. / Krueger, D. / Bak, A. / Eiermann, G. / He, J. / Cox, J. / Hicks, J. / Lyons, K. ...Authors: Biftu, T. / Sinha-Roy, R. / Chen, P. / Qian, X. / Feng, D. / Kuethe, J.T. / Scapin, G. / Gao, Y.D. / Yan, Y. / Krueger, D. / Bak, A. / Eiermann, G. / He, J. / Cox, J. / Hicks, J. / Lyons, K. / He, H. / Salituro, G. / Tong, S. / Patel, S. / Doss, G. / Petrov, A. / Wu, J. / Xu, S.S. / Sewall, C. / Zhang, X. / Zhang, B. / Thornberry, N.A. / Weber, A.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pnz.cif.gz | 349.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pnz.ent.gz | 280.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/4pnz ftp://data.pdbj.org/pub/pdb/validation_reports/pn/4pnz | HTTPS FTP |
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-Related structure data
Related structure data | 1x70S 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: 84476.648 Da / Num. of mol.: 2 / Fragment: extracellular domain (UNP residues 39-766) / Mutation: S39T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADCP2, CD26, DPP4 / Plasmid: Pbluebac4.5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV |
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-Sugars , 2 types, 13 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 #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 1627 molecules
#3: Chemical | ChemComp-NA / | ||
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#4: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20-25% PEG4000, 200 mM sodium acetate, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2009 |
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: 1.9→50 Å / Num. all: 160490 / Num. obs: 160170 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 25.51 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.566 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1X70 Resolution: 1.9→19.15 Å / Cor.coef. Fo:Fc: 0.9552 / Cor.coef. Fo:Fc free: 0.9418 / SU R Cruickshank DPI: 0.115 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.11 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0.187 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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