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Yorodumi- PDB-3c45: Human dipeptidyl peptidase IV/CD26 in complex with a fluoroolefin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c45 | ||||||||||||
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Title | Human dipeptidyl peptidase IV/CD26 in complex with a fluoroolefin inhibitor | ||||||||||||
Components | Dipeptidyl peptidase 4 soluble form | ||||||||||||
Keywords | HYDROLASE / ALPHA/BETA / BETA-PROPELLER / DIMER / Aminopeptidase / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane | ||||||||||||
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: 2.05 Å | ||||||||||||
Authors | Scapin, G. / Edmondson, S.D. / Weber, A.E. | ||||||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Fluoroolefins as amide bond mimics in dipeptidyl peptidase IV inhibitors Authors: Edmondson, S.D. / Wei, L. / Xu, J. / Shang, J. / Xu, S. / Pang, J. / Chaudhary, A. / Dean, D.C. / He, H. / Leiting, B. / Lyons, K.A. / Patel, R.A. / Patel, S.B. / Scapin, G. / Wu, J.K. / ...Authors: Edmondson, S.D. / Wei, L. / Xu, J. / Shang, J. / Xu, S. / Pang, J. / Chaudhary, A. / Dean, D.C. / He, H. / Leiting, B. / Lyons, K.A. / Patel, R.A. / Patel, S.B. / Scapin, G. / Wu, J.K. / Beconi, M.G. / 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 | 3c45.cif.gz | 335.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c45.ent.gz | 269.2 KB | Display | PDB format |
PDBx/mmJSON format | 3c45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c45 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c45 | HTTPS FTP |
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-Related structure data
Related structure data | 3c43C 1x70S 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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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: Catalytic domain / Mutation: S39T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Plasmid: PBLUEBAC4.5 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI5 / References: UniProt: P27487 |
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-Sugars , 2 types, 15 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: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 1018 molecules
#4: Chemical | ChemComp-NA / | ||
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#5: 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: 2.99 Å3/Da / Density % sol: 59.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG4000, SODIUM ACETATE, TRIS, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 / Wavelength: 1 Å | |||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2003 | |||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→50 Å / Num. all: 129506 / Num. obs: 128988 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.74 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.8 | |||||||||
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.56 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.2 / Num. unique all: 12762 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1X70 Resolution: 2.05→30 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å
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