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Open data
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Basic information
Entry | Database: PDB / ID: 5y7k | ||||||
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Title | Crystal structure of human DPP4 in complex with inhibitor1 | ||||||
![]() | Dipeptidyl peptidase 4 | ||||||
![]() | HYDROLASE / DPP4 / inhibitor | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, H.K. / Kim, E.E. | ||||||
![]() | ![]() Title: Unique binding mode of Evogliptin with human dipeptidyl peptidase IV. Authors: Lee, H.K. / Kim, M.K. / Kim, H.D. / Kim, H.J. / Kim, J.W. / Lee, J.O. / Kim, C.W. / Kim, E.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 591.4 KB | Display | ![]() |
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PDB format | ![]() | 488.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 100.1 KB | Display | |
Data in CIF | ![]() | 134.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y7hC ![]() 5y7jC ![]() 1x70S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 84462.617 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-8VU / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 20~28% (w/v) polyethylene glycol 4000, 0.1M HEPES or Tris pH 7.5~8.5 PH range: 7.5~8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.512→41.136 Å / Num. obs: 129816 / % possible obs: 97.7 % / Redundancy: 2.8 % / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.52→2.61 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.07 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X70 Resolution: 2.512→41.136 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.512→41.136 Å
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Refine LS restraints |
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LS refinement shell |
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