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Yorodumi- PDB-3hac: The structure of DPP-4 in complex with piperidine fused imidazopy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hac | ||||||||||||
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Title | The structure of DPP-4 in complex with piperidine fused imidazopyridine 34 | ||||||||||||
Components | Dipeptidyl peptidase 4 soluble form | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ALPHA/BETA / BETA-PROPELLER / DIMER / HYDROLASE / DIABETES / Aminopeptidase / Cell membrane / Disulfide bond / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane / HYDROLASE-HYDROLASE 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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||||||||
Authors | Scapin, G. | ||||||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Aminopiperidine-fused imidazoles as dipeptidyl peptidase-IV inhibitors Authors: Edmondson, S.D. / Mastracchio, A. / Cox, J.M. / Eiermann, G.J. / He, H. / Lyons, K.A. / Patel, R.A. / Patel, S.B. / Petrov, A. / Scapin, G. / Wu, J.K. / Xu, S. / Zhu, B. / Thornberry, N.A. / ...Authors: Edmondson, S.D. / Mastracchio, A. / Cox, J.M. / Eiermann, G.J. / He, H. / Lyons, K.A. / Patel, R.A. / Patel, S.B. / Petrov, A. / Scapin, G. / Wu, J.K. / Xu, S. / Zhu, B. / Thornberry, N.A. / Roy, R.S. / 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 | 3hac.cif.gz | 339.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hac.ent.gz | 272.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hac_validation.pdf.gz | 4 MB | Display | wwPDB validaton report |
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Full document | 3hac_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 3hac_validation.xml.gz | 64.4 KB | Display | |
Data in CIF | 3hac_validation.cif.gz | 96.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/3hac ftp://data.pdbj.org/pub/pdb/validation_reports/ha/3hac | HTTPS FTP |
-Related structure data
Related structure data | 3habC 1x70S 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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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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487 |
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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 #3: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 1209 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: 3 Å3/Da / Density % sol: 59.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, SODIUM ACETATE, 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: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2005 |
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→30 Å / Num. obs: 137116 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 30.1 Å2 / Rsym value: 0.095 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 1.3 / Num. unique all: 13341 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1X70 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.038 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.135 / 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: 35.435 Å2
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Refine analyze | Luzzati coordinate error obs: 0.238 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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