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Yorodumi- PDB-1wcy: Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wcy | |||||||||
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Title | Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Complex With Diprotin A | |||||||||
Components |
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Keywords | HYDROLASE / Serine protease / Dipeptidyl peptidase IV / CD26 / Prolyl oligopeptidase / BETA-propeller structure / Diprotin A | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Hiramatsu, H. / Yamamoto, A. / Kyono, K. / Higashiyama, Y. / Fukushima, C. / Shima, H. / Sugiyama, S. / Inaka, K. / Shimizu, R. | |||||||||
Citation | Journal: Biol.Chem. / Year: 2004 Title: The crystal structure of human dipeptidyl peptidase IV (DPPIV) complex with diprotin A Authors: Hiramatsu, H. / Yamamoto, A. / Kyono, K. / Higashiyama, Y. / Fukushima, C. / Shima, H. / Sugiyama, S. / Inaka, K. / Shimizu, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wcy.cif.gz | 337.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wcy.ent.gz | 271.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/1wcy ftp://data.pdbj.org/pub/pdb/validation_reports/wc/1wcy | HTTPS FTP |
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-Related structure data
Related structure data | 1j2eS 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 / Protein/peptide / Non-polymers , 3 types, 1241 molecules ABCD
#1: Protein | Mass: 85880.031 Da / Num. of mol.: 2 / Fragment: residues 33-772 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV #2: Protein/peptide | Mass: 341.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: The tripeptide was chemically synthesized #6: Water | ChemComp-HOH / | |
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-Sugars , 3 types, 12 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 18% PEG4000, 0.18M Sodium acetate, 0.18M Gly-NaOH, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 103739 / Num. obs: 103532 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J2E Resolution: 2.2→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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