+Open data
-Basic information
Entry | Database: PDB / ID: 5t4b | |||||||||
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Title | Human DPP4 in complex with a ligand 34a | |||||||||
Components | Dipeptidyl peptidase 4 | |||||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Structure-based drug design / diabetes / DPP4 inhibitors / hydrolase / 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 / response to hypoxia / cell adhesion / 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: 1.76 Å | |||||||||
Authors | Scapin, G. | |||||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2016 Title: Scaffold-hopping from xanthines to tricyclic guanines: A case study of dipeptidyl peptidase 4 (DPP4) inhibitors. Authors: Pissarnitski, D.A. / Zhao, Z. / Cole, D. / Wu, W.L. / Domalski, M. / Clader, J.W. / Scapin, G. / Voigt, J. / Soriano, A. / Kelly, T. / Powles, M.A. / Yao, Z. / Burnett, D.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t4b.cif.gz | 370.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t4b.ent.gz | 293.9 KB | Display | PDB format |
PDBx/mmJSON format | 5t4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t4b_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 5t4b_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 5t4b_validation.xml.gz | 76.1 KB | Display | |
Data in CIF | 5t4b_validation.cif.gz | 119.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/5t4b ftp://data.pdbj.org/pub/pdb/validation_reports/t4/5t4b | HTTPS FTP |
-Related structure data
Related structure data | 5t4eC 5t4fC 5t4hC 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 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, dipeptidyl-peptidase IV |
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-Sugars , 2 types, 12 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, 2240 molecules
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: 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: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.27-0.30 M sodium acetate 17-18% polyethylene glycol 3350 0.1 M tris hydrochloride pH 8.0 |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.76→55 Å / Num. obs: 200317 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.44 Å2 / Rsym value: 0.062 / Net I/σ(I): 18.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1X70 Resolution: 1.76→54.05 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9436 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.089
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Displacement parameters | Biso mean: 29.96 Å2
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Refine analyze | Luzzati coordinate error obs: 0.165 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→54.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.81 Å / Total num. of bins used: 20
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